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Towards v0.1.0 #62

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merged 44 commits into from
Nov 22, 2024
Merged

Towards v0.1.0 #62

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7d7c57e
first change in notebook
eroell Nov 2, 2024
09ce9b5
inspect why 2 omop dt fail on github ci
eroell Nov 4, 2024
54fe86e
inspect why 2 omop dt fail on github ci
eroell Nov 4, 2024
bebe595
inspect why 2 omop dt fail on github ci
eroell Nov 4, 2024
4c879a1
reduce redundancy; enhance docstrings
eroell Nov 4, 2024
3253c1a
fix paths
eroell Nov 4, 2024
c32c47e
towards more datasets
eroell Nov 4, 2024
7dc1903
load datasets with ehrapy's download function copied; cleaner table e…
eroell Nov 6, 2024
3f241fa
remove dataloader
eroell Nov 11, 2024
1f329ec
remove physio2012 stubs
eroell Nov 11, 2024
96a0740
merge physio2012
eroell Nov 11, 2024
3947f3a
switch to logging instead of prints
eroell Nov 11, 2024
ff0dd74
check individual connections to resolve synthea27nj
eroell Nov 11, 2024
66f232f
try to empty cache
eroell Nov 11, 2024
6a2e3ed
new test dir, undo workflows.yml
eroell Nov 11, 2024
e1a6abe
try different dir
eroell Nov 11, 2024
df3827a
improve download and datasets
eroell Nov 14, 2024
45f388e
fix pandas warning
eroell Nov 15, 2024
f4df4ff
use , delimiter in duckdb
eroell Nov 15, 2024
bbc663e
remove extract's from api.md
eroell Nov 15, 2024
839ff09
read w/ pandas instead of duckdb
eroell Nov 15, 2024
dafda91
support different capitalizations; check if pre-release fail again..?
eroell Nov 17, 2024
907c21f
remove load
eroell Nov 17, 2024
c91e401
remove some things I forgot
eroell Nov 17, 2024
a7c7af2
move validity checks to separate file
eroell Nov 17, 2024
09b0c34
enable and vanilla test for specimen table
eroell Nov 17, 2024
6854159
escape the % in duckdb's read_csv
eroell Nov 18, 2024
fcd641b
add robustness: empty observation,measurement,speciment acceptable
eroell Nov 18, 2024
a390b4c
add empty_observation test data
eroell Nov 18, 2024
adcf186
add support for start or end of e.g. drug_exposure
eroell Nov 18, 2024
afad702
pypots minimal demo
eroell Nov 20, 2024
929644a
add pypots to tutorial index
eroell Nov 21, 2024
3746c24
add one-hot presence encoding for a feature
eroell Nov 21, 2024
ac0c89b
add first basic interval-variable support for drug_exposure
eroell Nov 21, 2024
0933889
add strict tests for setup_variables
eroell Nov 21, 2024
5b38706
add tight test for interval vars drug_exposure table
eroell Nov 21, 2024
056340e
support condition_occurrence
eroell Nov 21, 2024
85b0c17
support procedure_occurrence
eroell Nov 22, 2024
6b0e57e
support device_exposure
eroell Nov 22, 2024
9dc6637
support drug_era
eroell Nov 22, 2024
0525855
support dose_era
eroell Nov 22, 2024
e4ad1db
support condition_era
eroell Nov 22, 2024
623ebab
support episode
eroell Nov 22, 2024
8b070c4
Refactor time interval table query function
eroell Nov 22, 2024
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11 changes: 0 additions & 11 deletions docs/api.md
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,17 +23,6 @@
io.omop.setup_obs
io.omop.setup_variables
io.omop.get_time_interval_table
io.omop.load
io.omop.extract_person
io.omop.extract_observation_period
io.omop.extract_measurement
io.omop.extract_observation
io.omop.extract_procedure_occurrence
io.omop.extract_specimen
io.omop.extract_device_exposure
io.omop.extract_drug_exposure
io.omop.extract_condition_occurrence
io.omop.extract_note
```

## Datasets
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1 change: 1 addition & 0 deletions docs/index.md
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Original file line number Diff line number Diff line change
Expand Up @@ -16,4 +16,5 @@ notebooks/omop_tables_tutorial
notebooks/cohort_definition
notebooks/study_design_example_omop_cdm
notebooks/indwelling_arterial_catheters
notebooks/tutorial_time_series_with_pypots
```
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