Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Bump requirement pins #192

Merged
merged 5 commits into from
Jan 2, 2025
Merged

Bump requirement pins #192

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
8f1cb35
Bump requirement pins
mmore500 Jan 2, 2025
8971b26
Configu max columns a simpler way
mmore500 Jan 2, 2025
16e6f15
Fix out of bounds access error
mmore500 Jan 2, 2025
43ffa2f
Fix elipses
mmore500 Jan 2, 2025
ab82e9a
Log sort_by time separately
mmore500 Jan 2, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion hstrat/_auxiliary_lib/_render_polars_snapshot.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ def render_polars_snapshot(
The rendered DataFrame, as a string, if `display` is not used.
"""
with pl.Config() as cfg:
cfg.set_tbl_cols(df.lazy().collect_schema().len())
cfg.set_tbl_cols(-1)
head = repr(df.lazy().head().collect())
message = " ".join(
[
Expand Down
11 changes: 9 additions & 2 deletions hstrat/dataframe/_surface_unpack_reconstruct.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,14 @@ def _build_records_chunked(
):
long_df = dstream_dataframe.explode_lookup_unpacked(
df_slice, value_type="uint64"
).select(
)

with log_context_duration(
'.sort_by("dstream_Tbar").over(partition_by="dstream_data_id") '
f"({i + 1}/{num_slices})",
logging.info,
):
long_df = long_df.select(
pl.col(
"dstream_data_id",
"dstream_T",
Expand Down Expand Up @@ -264,7 +271,7 @@ def surface_unpack_reconstruct(
res["dstream_S"] = pd.Series(dtype=int)
return pl.from_pandas(res)

logging.info("extracting metadata..")
logging.info("extracting metadata...")
dstream_storage_bitwidth = get_sole_scalar_value_polars(
df, "dstream_storage_bitwidth"
)
Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ dependencies = [
"bitstring>=3.1.9",
"dendropy>=4.5.2",
"Deprecated>=1.2.13",
"downstream>=1.4.0",
"downstream>=1.5.1",
"iterpop>=0.3.4",
"interval_search>=0.3.1",
"joinem>=0.9.1",
Expand Down
4 changes: 3 additions & 1 deletion requirements-dev/py310/requirements-all.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ docutils==0.21.2
# readme-renderer
# sphinx
# sphinx-rtd-theme
downstream==1.4.0
downstream==1.5.1
# via hstrat (../../pyproject.toml)
entrypoints==0.3
# via flake8
Expand Down Expand Up @@ -304,6 +304,8 @@ polars==1.16.0
# hstrat (../../pyproject.toml)
# downstream
# joinem
polars-u64-idx==1.18.0
# via hstrat (../../pyproject.toml)
prettytable==3.12.0
# via hstrat (../../pyproject.toml)
prompt-toolkit==3.0.48
Expand Down
4 changes: 3 additions & 1 deletion requirements-dev/py310/requirements-docs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ docutils==0.21.2
# nbsphinx
# sphinx
# sphinx-rtd-theme
downstream==1.4.0
downstream==1.5.1
# via hstrat (../../pyproject.toml)
ete3==3.1.3
# via alifedata-phyloinformatics-convert
Expand Down Expand Up @@ -239,6 +239,8 @@ polars==1.16.0
# hstrat (../../pyproject.toml)
# downstream
# joinem
polars-u64-idx==1.18.0
# via hstrat (../../pyproject.toml)
prettytable==3.12.0
# via hstrat (../../pyproject.toml)
prompt-toolkit==3.0.48
Expand Down
4 changes: 3 additions & 1 deletion requirements-dev/py310/requirements-jit.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ deprecated==1.2.15
# via
# hstrat (../../pyproject.toml)
# alifedata-phyloinformatics-convert
downstream==1.4.0
downstream==1.5.1
# via hstrat (../../pyproject.toml)
ete3==3.1.3
# via alifedata-phyloinformatics-convert
Expand Down Expand Up @@ -145,6 +145,8 @@ polars==1.16.0
# hstrat (../../pyproject.toml)
# downstream
# joinem
polars-u64-idx==1.18.0
# via hstrat (../../pyproject.toml)
prettytable==3.12.0
# via hstrat (../../pyproject.toml)
propcache==0.2.0
Expand Down
4 changes: 3 additions & 1 deletion requirements-dev/py310/requirements-minimal.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@ deprecated==1.2.15
# via
# hstrat (../../pyproject.toml)
# alifedata-phyloinformatics-convert
downstream==1.4.0
downstream==1.5.1
# via hstrat (../../pyproject.toml)
ete3==3.1.3
# via alifedata-phyloinformatics-convert
Expand Down Expand Up @@ -132,6 +132,8 @@ polars==1.16.0
# hstrat (../../pyproject.toml)
# downstream
# joinem
polars-u64-idx==1.18.0
# via hstrat (../../pyproject.toml)
prettytable==3.12.0
# via hstrat (../../pyproject.toml)
propcache==0.2.0
Expand Down
4 changes: 3 additions & 1 deletion requirements-dev/py310/requirements-release.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ deprecated==1.2.15
# alifedata-phyloinformatics-convert
docutils==0.21.2
# via readme-renderer
downstream==1.4.0
downstream==1.5.1
# via hstrat (../../pyproject.toml)
ete3==3.1.3
# via alifedata-phyloinformatics-convert
Expand Down Expand Up @@ -154,6 +154,8 @@ polars==1.16.0
# hstrat (../../pyproject.toml)
# downstream
# joinem
polars-u64-idx==1.18.0
# via hstrat (../../pyproject.toml)
prettytable==3.12.0
# via hstrat (../../pyproject.toml)
propcache==0.2.0
Expand Down
4 changes: 3 additions & 1 deletion requirements-dev/py310/requirements-testing.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ deprecated==1.2.15
# alifedata-phyloinformatics-convert
distlib==0.3.9
# via virtualenv
downstream==1.4.0
downstream==1.5.1
# via hstrat (../../pyproject.toml)
entrypoints==0.3
# via flake8
Expand Down Expand Up @@ -183,6 +183,8 @@ polars==1.16.0
# hstrat (../../pyproject.toml)
# downstream
# joinem
polars-u64-idx==1.18.0
# via hstrat (../../pyproject.toml)
prettytable==3.12.0
# via hstrat (../../pyproject.toml)
propcache==0.2.0
Expand Down
4 changes: 3 additions & 1 deletion requirements-dev/py311/requirements-all.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ docutils==0.21.2
# readme-renderer
# sphinx
# sphinx-rtd-theme
downstream==1.4.0
downstream==1.5.1
# via hstrat (../../pyproject.toml)
entrypoints==0.3
# via flake8
Expand Down Expand Up @@ -302,6 +302,8 @@ polars==1.16.0
# hstrat (../../pyproject.toml)
# downstream
# joinem
polars-u64-idx==1.18.0
# via hstrat (../../pyproject.toml)
prettytable==3.12.0
# via hstrat (../../pyproject.toml)
prompt-toolkit==3.0.48
Expand Down
4 changes: 3 additions & 1 deletion requirements-dev/py311/requirements-docs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ docutils==0.21.2
# nbsphinx
# sphinx
# sphinx-rtd-theme
downstream==1.4.0
downstream==1.5.1
# via hstrat (../../pyproject.toml)
ete3==3.1.3
# via alifedata-phyloinformatics-convert
Expand Down Expand Up @@ -239,6 +239,8 @@ polars==1.16.0
# hstrat (../../pyproject.toml)
# downstream
# joinem
polars-u64-idx==1.18.0
# via hstrat (../../pyproject.toml)
prettytable==3.12.0
# via hstrat (../../pyproject.toml)
prompt-toolkit==3.0.48
Expand Down
4 changes: 3 additions & 1 deletion requirements-dev/py311/requirements-jit.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ deprecated==1.2.15
# via
# hstrat (../../pyproject.toml)
# alifedata-phyloinformatics-convert
downstream==1.4.0
downstream==1.5.1
# via hstrat (../../pyproject.toml)
ete3==3.1.3
# via alifedata-phyloinformatics-convert
Expand Down Expand Up @@ -145,6 +145,8 @@ polars==1.16.0
# hstrat (../../pyproject.toml)
# downstream
# joinem
polars-u64-idx==1.18.0
# via hstrat (../../pyproject.toml)
prettytable==3.12.0
# via hstrat (../../pyproject.toml)
propcache==0.2.0
Expand Down
4 changes: 3 additions & 1 deletion requirements-dev/py311/requirements-minimal.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@ deprecated==1.2.15
# via
# hstrat (../../pyproject.toml)
# alifedata-phyloinformatics-convert
downstream==1.4.0
downstream==1.5.1
# via hstrat (../../pyproject.toml)
ete3==3.1.3
# via alifedata-phyloinformatics-convert
Expand Down Expand Up @@ -132,6 +132,8 @@ polars==1.16.0
# hstrat (../../pyproject.toml)
# downstream
# joinem
polars-u64-idx==1.18.0
# via hstrat (../../pyproject.toml)
prettytable==3.12.0
# via hstrat (../../pyproject.toml)
propcache==0.2.0
Expand Down
4 changes: 3 additions & 1 deletion requirements-dev/py311/requirements-release.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ deprecated==1.2.15
# alifedata-phyloinformatics-convert
docutils==0.21.2
# via readme-renderer
downstream==1.4.0
downstream==1.5.1
# via hstrat (../../pyproject.toml)
ete3==3.1.3
# via alifedata-phyloinformatics-convert
Expand Down Expand Up @@ -154,6 +154,8 @@ polars==1.16.0
# hstrat (../../pyproject.toml)
# downstream
# joinem
polars-u64-idx==1.18.0
# via hstrat (../../pyproject.toml)
prettytable==3.12.0
# via hstrat (../../pyproject.toml)
propcache==0.2.0
Expand Down
4 changes: 3 additions & 1 deletion requirements-dev/py311/requirements-testing.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ deprecated==1.2.15
# alifedata-phyloinformatics-convert
distlib==0.3.9
# via virtualenv
downstream==1.4.0
downstream==1.5.1
# via hstrat (../../pyproject.toml)
entrypoints==0.3
# via flake8
Expand Down Expand Up @@ -181,6 +181,8 @@ polars==1.16.0
# hstrat (../../pyproject.toml)
# downstream
# joinem
polars-u64-idx==1.18.0
# via hstrat (../../pyproject.toml)
prettytable==3.12.0
# via hstrat (../../pyproject.toml)
propcache==0.2.0
Expand Down
4 changes: 3 additions & 1 deletion requirements-dev/py312/requirements-all.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ docutils==0.21.2
# readme-renderer
# sphinx
# sphinx-rtd-theme
downstream==1.4.0
downstream==1.5.1
# via hstrat (../../pyproject.toml)
entrypoints==0.3
# via flake8
Expand Down Expand Up @@ -302,6 +302,8 @@ polars==1.16.0
# hstrat (../../pyproject.toml)
# downstream
# joinem
polars-u64-idx==1.18.0
# via hstrat (../../pyproject.toml)
prettytable==3.12.0
# via hstrat (../../pyproject.toml)
prompt-toolkit==3.0.48
Expand Down
4 changes: 3 additions & 1 deletion requirements-dev/py312/requirements-docs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ docutils==0.21.2
# nbsphinx
# sphinx
# sphinx-rtd-theme
downstream==1.4.0
downstream==1.5.1
# via hstrat (../../pyproject.toml)
ete3==3.1.3
# via alifedata-phyloinformatics-convert
Expand Down Expand Up @@ -239,6 +239,8 @@ polars==1.16.0
# hstrat (../../pyproject.toml)
# downstream
# joinem
polars-u64-idx==1.18.0
# via hstrat (../../pyproject.toml)
prettytable==3.12.0
# via hstrat (../../pyproject.toml)
prompt-toolkit==3.0.48
Expand Down
6 changes: 4 additions & 2 deletions requirements-dev/py312/requirements-jit.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# This file was autogenerated by uv via the following command:
# uv pip compile --python-version=3.11 ../../pyproject.toml --extra jit -o requirements-jit.txt
# uv pip compile --python-version=3.12 ../../pyproject.toml --extra jit -o requirements-jit.txt
alifedata-phyloinformatics-convert==0.17.0
# via hstrat (../../pyproject.toml)
annotated-types==0.7.0
Expand Down Expand Up @@ -36,7 +36,7 @@ deprecated==1.2.15
# via
# hstrat (../../pyproject.toml)
# alifedata-phyloinformatics-convert
downstream==1.4.0
downstream==1.5.1
# via hstrat (../../pyproject.toml)
ete3==3.1.3
# via alifedata-phyloinformatics-convert
Expand Down Expand Up @@ -145,6 +145,8 @@ polars==1.16.0
# hstrat (../../pyproject.toml)
# downstream
# joinem
polars-u64-idx==1.18.0
# via hstrat (../../pyproject.toml)
prettytable==3.12.0
# via hstrat (../../pyproject.toml)
propcache==0.2.0
Expand Down
4 changes: 3 additions & 1 deletion requirements-dev/py312/requirements-minimal.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@ deprecated==1.2.15
# via
# hstrat (../../pyproject.toml)
# alifedata-phyloinformatics-convert
downstream==1.4.0
downstream==1.5.1
# via hstrat (../../pyproject.toml)
ete3==3.1.3
# via alifedata-phyloinformatics-convert
Expand Down Expand Up @@ -132,6 +132,8 @@ polars==1.16.0
# hstrat (../../pyproject.toml)
# downstream
# joinem
polars-u64-idx==1.18.0
# via hstrat (../../pyproject.toml)
prettytable==3.12.0
# via hstrat (../../pyproject.toml)
propcache==0.2.0
Expand Down
4 changes: 3 additions & 1 deletion requirements-dev/py312/requirements-release.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ deprecated==1.2.15
# alifedata-phyloinformatics-convert
docutils==0.21.2
# via readme-renderer
downstream==1.4.0
downstream==1.5.1
# via hstrat (../../pyproject.toml)
ete3==3.1.3
# via alifedata-phyloinformatics-convert
Expand Down Expand Up @@ -154,6 +154,8 @@ polars==1.16.0
# hstrat (../../pyproject.toml)
# downstream
# joinem
polars-u64-idx==1.18.0
# via hstrat (../../pyproject.toml)
prettytable==3.12.0
# via hstrat (../../pyproject.toml)
propcache==0.2.0
Expand Down
4 changes: 3 additions & 1 deletion requirements-dev/py312/requirements-testing.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ deprecated==1.2.15
# alifedata-phyloinformatics-convert
distlib==0.3.9
# via virtualenv
downstream==1.4.0
downstream==1.5.1
# via hstrat (../../pyproject.toml)
entrypoints==0.3
# via flake8
Expand Down Expand Up @@ -181,6 +181,8 @@ polars==1.16.0
# hstrat (../../pyproject.toml)
# downstream
# joinem
polars-u64-idx==1.18.0
# via hstrat (../../pyproject.toml)
prettytable==3.12.0
# via hstrat (../../pyproject.toml)
propcache==0.2.0
Expand Down
4 changes: 2 additions & 2 deletions tests/test_hstrat/test_dataframe/assets/packed.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
awoo,dstream_algo,downstream_version,data_hex,dstream_storage_bitoffset,dstream_storage_bitwidth,dstream_T_bitoffset,dstream_T_bitwidth,dstream_S
bar,dstream.steady_algo,1.0.1,080001030702050406,8,96,0,8,8
baz,dstream.steady_algo,1.0.1,0b0001030702050906,8,96,0,8,8
bar,dstream.steady_algo,1.0.1,080001030702050406,8,64,0,8,8
baz,dstream.steady_algo,1.0.1,0b0001030702050906,8,64,0,8,8
Loading