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CU-8694gzbn3 k fold metrics #432

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merged 55 commits into from
Jun 19, 2024
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35a66f3
CU-8694gzbud: Add context manager that is able to snapshot CDB state
mart-r May 8, 2024
df8459b
CU-8694gzbud: Add tests to snapshotting CDB state
mart-r May 8, 2024
20a403e
CU-8694gzbud: Refactor tests for CDB state snapshotting
mart-r May 8, 2024
557602b
CU-8694gzbud: Remove use of deprecated method in CDB utils and use no…
mart-r May 8, 2024
16e875b
CU-8694gzbud: Add tests for training and CDB state capturing
mart-r May 8, 2024
0294fea
CU-8694gzbud: Small refactor in tests
mart-r May 8, 2024
cc2bcf5
CU-8694gzbud: Add option to save state on disk
mart-r May 8, 2024
8b19609
CU-8694gzbud: Add debug logging output when saving state on disk
mart-r May 8, 2024
3017067
CU-8694gzbud: Remove unused import
mart-r May 8, 2024
de74d0c
CU-8694gzbud: Add tests for disk-based state save
mart-r May 9, 2024
4a269ab
CU-8694gzbud: Move CDB state code to its own module
mart-r May 9, 2024
bfcff96
CU-8694gzbud: Remove unused import
mart-r May 9, 2024
c0ba2b9
CU-8694gzbud: Add doc strings to methods
mart-r May 9, 2024
da585f5
CU-8694gzbx4: Small optimisation for stats
mart-r May 9, 2024
50ae4d7
CU-8694gzbx4: Add MCTExport related module
mart-r May 10, 2024
b51117d
CU-8694gzbx4: Add MCTExport related tests
mart-r May 10, 2024
c9944d3
CU-8694gzbx4: Add code for k-fold statistics
mart-r May 10, 2024
bad5936
CU-8694gzbx4: Add tests for k-fold statistics
mart-r May 10, 2024
988905c
CU-8694gzbx4: Add test-MCT export with fake concepts
mart-r May 10, 2024
b8c4ff4
CU-8694gzbx4: Fix a doc string
mart-r May 10, 2024
bfdb4ca
CU-8694gzbx4: Fix types in MCT export module
mart-r May 10, 2024
df2bde7
CU-8694gzbx4: Fix types in k-fold module
mart-r May 10, 2024
08a2d0d
CU-8694gzbx4: Remove accidentally committed test class
mart-r May 10, 2024
05eb171
CU-8694gzbn3: Add missing test helper file
mart-r May 11, 2024
383c929
CU-8694gzbn3: Remove whitespace change from otherwise uncahnged file
mart-r May 11, 2024
48ce03e
CU-8694gzbn3: Allow 5 minutes longer for tests
mart-r May 11, 2024
316ec76
CU-8694gzbn3: Move to python 3.8-compatible typed dict
mart-r May 11, 2024
716e939
CU-8694gzbn3: Add more time for tests in worklow (now 30 minutes)
mart-r May 12, 2024
5be04d2
CU-8694gzbn3: Add more time for tests in worklow (now 45 minutes)
mart-r May 13, 2024
9459b8d
CU-8694gzbn3: Update test-pypi timeout to 45 minutes
mart-r May 13, 2024
3618b9c
CU-8694gzbn3: Remove timeout from unit tests in main workflow
mart-r May 13, 2024
94bce56
CU-8694gzbn3: Make tests stop upon first failure
mart-r May 13, 2024
666c013
CU-8694gzbn3: Fix test stop upon first failure (arg/option order)
mart-r May 13, 2024
8c5c0d0
CU-8694gzbn3: Remove debug code and old comments
mart-r May 13, 2024
e6debce
CU-8694gzbn3: Remove all timeouts from main workflow
mart-r May 13, 2024
abd8d0b
CU-8694gzbn3: Remove more old / useless comments in tests
mart-r May 14, 2024
03531da
CU-8694gzbn3: Add debug output when running k-fold tests to see where…
mart-r May 14, 2024
12c519a
CU-8694gzbn3: Add debug output when ANY tests to see where it may be …
mart-r May 14, 2024
9b02925
CU-8694gzbn3: Remove explicit debug output from k-fold test cases
mart-r May 14, 2024
faaf7fb
CU-8694gzbn3: Remove timeouts from DEID tests in case they're the one…
mart-r May 14, 2024
f0b2cf0
GHA/test fixes (#437)
mart-r May 16, 2024
afd093c
CU-8694gzbn3: Remove legacy / archived / unused tests
mart-r May 16, 2024
f1968d3
Merge branch 'master' into CU-8694gzbn3-k-fold-metrics
mart-r May 16, 2024
8356f16
Merge branch 'master' into CU-8694gzbn3-k-fold-metrics
mart-r May 22, 2024
db2c549
CU-8694gzbn3: Add doc strings for FoldCreator init
mart-r May 22, 2024
07b5b54
Merge branch 'master' into CU-8694gzbn3-k-fold-metrics
mart-r May 24, 2024
79d5983
CU-8694gzbn3: Move to a split-type enum
mart-r May 24, 2024
b01132f
CU-8694gzbn3: Add documentation to split-type enum
mart-r May 24, 2024
fdac749
CU-8694gzbn3: Create separate fold creators for different types of sp…
mart-r May 24, 2024
6430ba3
CU-8694gzbn3: Resort document order in test time nullification process
mart-r May 24, 2024
70b1c2e
CU-8694gzbn3: Add option to count number of annotations in doc for MC…
mart-r May 24, 2024
3680105
CU-8694gzbn3: Add weighted documents based split option along with re…
mart-r May 24, 2024
a40b456
CU-8694gzbn3: Update default fold creation split type to weighted doc…
mart-r May 24, 2024
f79aa3d
CU-8694gzbn3: Add test to ensure weighted documents split creates a r…
mart-r May 24, 2024
439f62d
Merge branch 'master' into CU-8694gzbn3-k-fold-metrics
mart-r Jun 19, 2024
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10 changes: 8 additions & 2 deletions .github/workflows/main.yml
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,13 @@ jobs:
flake8 medcat
- name: Test
run: |
timeout 17m python -m unittest discover
all_files=$(git ls-files | grep '^tests/.*\.py$' | grep -v '/__init__\.py$' | sed 's/\.py$//' | sed 's/\//./g')
num_files=$(echo "$all_files" | wc -l)
midpoint=$((num_files / 2))
first_half_nl=$(echo "$all_files" | head -n $midpoint)
second_half_nl=$(echo "$all_files" | tail -n +$(($midpoint + 1)))
timeout 25m python -m unittest ${first_half_nl[@]}
timeout 25m python -m unittest ${second_half_nl[@]}

publish-to-test-pypi:

Expand All @@ -43,7 +49,7 @@ jobs:
github.event_name == 'push' &&
startsWith(github.ref, 'refs/tags') != true
runs-on: ubuntu-20.04
timeout-minutes: 20
timeout-minutes: 45
concurrency: publish-to-test-pypi
needs: [build]

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