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f58ec7d
Polars fix bug of OOM on large table join
Logiquo Nov 27, 2025
c196a8b
Fix type hint
Logiquo Nov 27, 2025
8602c0d
Add cache_dir
Logiquo Nov 27, 2025
0ceeea9
Remove to_lower as this is a no-op
Logiquo Nov 27, 2025
996b35c
Add caching behaviour
Logiquo Nov 27, 2025
6991f26
Add test case
Logiquo Nov 27, 2025
a36a819
Add StreamingParquetWriter
Logiquo Nov 27, 2025
4d95ce5
write samples
Logiquo Nov 27, 2025
4f26c1d
Add SampleBuilder
Logiquo Nov 27, 2025
2ad809d
Fix Mimic4
Logiquo Nov 27, 2025
45ae343
fix incorrect dev mode
Logiquo Dec 5, 2025
b4949ec
change fit to take Iterator
Logiquo Dec 5, 2025
0494bca
update test
Logiquo Dec 5, 2025
e63d500
rename
Logiquo Dec 5, 2025
525c526
update fit to use Iterable
Logiquo Dec 5, 2025
6caa917
Fix SampleBuilder
Logiquo Dec 5, 2025
8a40d3b
Fix tsv test
Logiquo Dec 5, 2025
504aaa2
Fix base dataset test
Logiquo Dec 5, 2025
6c9363a
cache processed data
Logiquo Dec 5, 2025
a42c131
save schema for SampleBuilder
Logiquo Dec 6, 2025
8f027ae
Fix sampledataset
Logiquo Dec 6, 2025
9578424
Fix multi-worker crashes
Logiquo Dec 6, 2025
830259a
update test
Logiquo Dec 6, 2025
3652e2d
Fix non-pickable
Logiquo Dec 6, 2025
174d53f
Fix get_dataloader
Logiquo Dec 6, 2025
302cb22
Fix embedding
Logiquo Dec 6, 2025
b754b4f
support split
Logiquo Dec 6, 2025
34ba3f2
Fix test
Logiquo Dec 6, 2025
340902b
Fix collate_fn
Logiquo Dec 6, 2025
ba348c1
fix conflicting cache dir
Logiquo Dec 6, 2025
c0fd0cc
update test
Logiquo Dec 7, 2025
0010409
add create_sample_dataset to convert list of samples to SampleDataset
Logiquo Dec 7, 2025
a3798f8
test new dataset
Logiquo Dec 7, 2025
53079e8
Update docs
Logiquo Dec 7, 2025
e36eae3
Fix test
Logiquo Dec 7, 2025
17304d9
Merge remote-tracking branch 'upstream/master' into mem-7
Logiquo Dec 7, 2025
5522ea3
Merge remote-tracking branch 'upstream/master' into mem-7
Logiquo Dec 7, 2025
2bf7342
Fix test
Logiquo Dec 7, 2025
091a22d
Fix test
Logiquo Dec 7, 2025
f858748
Fix test
Logiquo Dec 7, 2025
eae7212
Fix test
Logiquo Dec 7, 2025
a4b176f
add InMemorySampleDataset
Logiquo Dec 7, 2025
316b09c
support InMemorySampleDataset
Logiquo Dec 7, 2025
d091341
Fix test
Logiquo Dec 7, 2025
fe5a769
Fix tests
Logiquo Dec 7, 2025
be1e74a
Fix test
Logiquo Dec 7, 2025
8dc1acd
Fix test
Logiquo Dec 7, 2025
b1539ca
support set_shuffle for InMemorySampleDataset
Logiquo Dec 7, 2025
7e701a1
Fix in memory dataset subset
Logiquo Dec 8, 2025
68a7ea9
Fix test
Logiquo Dec 8, 2025
8b67469
update sample dataset test
Logiquo Dec 8, 2025
29908db
Add deps
Logiquo Dec 8, 2025
24facac
Fix test
Logiquo Dec 8, 2025
7747529
commit for fixing model docs
jhnwu3 Dec 8, 2025
ea47052
fix adacare docstrings
jhnwu3 Dec 8, 2025
4543dec
fix for python 3.10 override typing incompatibility, but still strugg…
jhnwu3 Dec 8, 2025
73fb321
organize for benchmarking scripts
jhnwu3 Dec 8, 2025
fe744dc
add deps
Logiquo Dec 10, 2025
f6bc340
add _scan_csv_tsv_gz
Logiquo Dec 10, 2025
4e23666
convert load_table to dask
Logiquo Dec 10, 2025
ecec90d
convert load_data to dask
Logiquo Dec 10, 2025
ff0b502
convert global_event_df to dask
Logiquo Dec 10, 2025
3830268
Fix base dataset test
Logiquo Dec 10, 2025
73aa3a8
Fix bug
Logiquo Dec 10, 2025
668f4de
Fixup
Logiquo Dec 10, 2025
ebcabc5
Fixup
Logiquo Dec 10, 2025
d8e2383
fixup
Logiquo Dec 10, 2025
aa64e99
main guard
Logiquo Dec 11, 2025
763f358
fix incorrect null value handling
Logiquo Dec 11, 2025
bd92ba7
change back to ms to mimic old pyhealth beahviour
Logiquo Dec 11, 2025
466d95e
add TODO
Logiquo Dec 11, 2025
87b171f
main guard check
Logiquo Dec 13, 2025
e77e08b
fix nullable issue?
Logiquo Dec 13, 2025
49b3b64
revert change
Logiquo Dec 13, 2025
afcd0f2
Merge remote-tracking branch 'upstream/master' into mem-9
Logiquo Dec 13, 2025
7748307
update API layers
Logiquo Dec 14, 2025
f6a582b
Fix cache test
Logiquo Dec 14, 2025
7c7e5e4
support remote url
Logiquo Dec 14, 2025
cfa87be
fix test
Logiquo Dec 14, 2025
264a026
fix incorrect type in nw
Logiquo Dec 14, 2025
045d2ad
less worker
Logiquo Dec 15, 2025
5b000b1
non-dev for memtest
Logiquo Dec 15, 2025
44c185f
fix incorrect behaviour on notebook & make sure dask excption throw a…
Logiquo Dec 16, 2025
54db875
update on installation details and recommended settings for use with …
jhnwu3 Dec 17, 2025
9e994bd
additional clarifications here
jhnwu3 Dec 17, 2025
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40 changes: 40 additions & 0 deletions docs/install.rst
Original file line number Diff line number Diff line change
@@ -1,6 +1,10 @@
Installation
============

**Python Version Recommendation**

We recommend using **Python 3.12** for optimal parallel processing and memory management performance. While PyHealth supports Python 3.8+, Python 3.12 provides significant improvements in these areas.

**Recommended Installation (Alpha Version)**

We recommend installing the latest alpha version from PyPi, which offers significant improvements in performance:
Expand Down Expand Up @@ -67,4 +71,40 @@ For example, if you use NVIDIA RTX A6000 as your GPU for training, you should in

conda install pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch.

----

**Platform-Specific Notes**

**Windows Subsystem for Linux (WSL)**

When using PyHealth on WSL, you **may need to** disable swap memory due to a bug in how Dask interacts with WSL's memory management when memory runs out. This prevents performance issues and potential crashes.

**Method 1: Using WSL Settings App (Windows 11)**

1. Open the WSL Settings app in Windows
2. Navigate to Memory and Processor settings
3. Set Swap size to 0 MB
4. Apply changes and restart WSL

**Method 2: Manual Configuration**

1. Open PowerShell as Administrator
2. Create or edit `%UserProfile%\.wslconfig` file
3. Add the following configuration:

.. code-block:: ini

[wsl2]
swap=0

4. Restart WSL by running in PowerShell: ``wsl --shutdown``

**Other Platforms**

PyHealth should work without additional configuration on:

- Linux (native)
- macOS
- Windows (with proper Python installation)

----
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