-
Notifications
You must be signed in to change notification settings - Fork 23
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #418 from ahernank/417-fix-tests-after-year-change
Update cohorts version & expected frq col
- Loading branch information
Showing
3 changed files
with
95 additions
and
95 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,44 +1,44 @@ | ||
name: notebooks | ||
on: | ||
push: | ||
branches: | ||
- master | ||
pull_request: | ||
branches: | ||
- master | ||
push: | ||
branches: | ||
- master | ||
pull_request: | ||
branches: | ||
- master | ||
jobs: | ||
notebooks: | ||
strategy: | ||
fail-fast: true | ||
runs-on: ubuntu-latest | ||
steps: | ||
- name: Checkout source | ||
uses: actions/checkout@v3 | ||
notebooks: | ||
strategy: | ||
fail-fast: true | ||
runs-on: ubuntu-latest | ||
steps: | ||
- name: Checkout source | ||
uses: actions/checkout@v3 | ||
|
||
- name: Install poetry | ||
run: pipx install poetry==1.4.2 | ||
- name: Install poetry | ||
run: pipx install poetry==1.4.2 | ||
|
||
- name: Setup python | ||
uses: actions/setup-python@v4 | ||
with: | ||
python-version: '3.11' | ||
cache: 'poetry' | ||
- name: Setup python | ||
uses: actions/setup-python@v4 | ||
with: | ||
python-version: "3.11" | ||
cache: "poetry" | ||
|
||
- name: Install dependencies | ||
run: poetry install | ||
- name: Install dependencies | ||
run: poetry install | ||
|
||
- name: Restore GCS cache | ||
uses: actions/cache/restore@v3 | ||
with: | ||
path: gcs_cache | ||
key: gcs_cache_notebooks_20230425 | ||
- name: Restore GCS cache | ||
uses: actions/cache/restore@v3 | ||
with: | ||
path: gcs_cache | ||
key: gcs_cache_notebooks_20230811 | ||
|
||
- name: Run notebooks | ||
run: poetry run jupyter nbconvert --execute notebooks/* --inplace | ||
- name: Run notebooks | ||
run: poetry run jupyter nbconvert --execute notebooks/* --inplace | ||
|
||
- name: Save GCS cache | ||
uses: actions/cache/save@v3 | ||
if: always() | ||
with: | ||
path: gcs_cache | ||
key: gcs_cache_notebooks_20230425 | ||
- name: Save GCS cache | ||
uses: actions/cache/save@v3 | ||
if: always() | ||
with: | ||
path: gcs_cache | ||
key: gcs_cache_notebooks_20230811 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,51 +1,51 @@ | ||
name: tests | ||
on: | ||
push: | ||
branches: | ||
- master | ||
pull_request: | ||
branches: | ||
- master | ||
push: | ||
branches: | ||
- master | ||
pull_request: | ||
branches: | ||
- master | ||
jobs: | ||
tests: | ||
strategy: | ||
fail-fast: true | ||
matrix: | ||
python-version: ['3.8', '3.9', '3.10', '3.11'] | ||
runs-on: ubuntu-latest | ||
steps: | ||
- name: Checkout source | ||
uses: actions/checkout@v3 | ||
tests: | ||
strategy: | ||
fail-fast: true | ||
matrix: | ||
python-version: ["3.8", "3.9", "3.10", "3.11"] | ||
runs-on: ubuntu-latest | ||
steps: | ||
- name: Checkout source | ||
uses: actions/checkout@v3 | ||
|
||
- name: Install poetry | ||
run: pipx install poetry==1.4.2 | ||
- name: Install poetry | ||
run: pipx install poetry==1.4.2 | ||
|
||
- name: Setup python | ||
uses: actions/setup-python@v4 | ||
with: | ||
python-version: ${{ matrix.python-version }} | ||
cache: 'poetry' | ||
- name: Setup python | ||
uses: actions/setup-python@v4 | ||
with: | ||
python-version: ${{ matrix.python-version }} | ||
cache: "poetry" | ||
|
||
- name: Install dependencies | ||
run: poetry install | ||
- name: Install dependencies | ||
run: poetry install | ||
|
||
# Run a subset of tests first which run quickly without accessing | ||
# any remote data in order to fail fast where possible. | ||
- name: Run fast unit tests | ||
run: poetry run pytest -v tests/anoph --typeguard-packages=malariagen_data,malariagen_data.anoph | ||
# Run a subset of tests first which run quickly without accessing | ||
# any remote data in order to fail fast where possible. | ||
- name: Run fast unit tests | ||
run: poetry run pytest -v tests/anoph --typeguard-packages=malariagen_data,malariagen_data.anoph | ||
|
||
- name: Restore GCS cache | ||
uses: actions/cache/restore@v3 | ||
with: | ||
path: gcs_cache | ||
key: gcs_cache_tests_20230420 | ||
- name: Restore GCS cache | ||
uses: actions/cache/restore@v3 | ||
with: | ||
path: gcs_cache | ||
key: gcs_cache_tests_20230811 | ||
|
||
- name: Run full test suite | ||
run: poetry run pytest -v tests | ||
- name: Run full test suite | ||
run: poetry run pytest -v tests | ||
|
||
- name: Save GCS cache | ||
uses: actions/cache/save@v3 | ||
if: always() | ||
with: | ||
path: gcs_cache | ||
key: gcs_cache_tests_20230420 | ||
- name: Save GCS cache | ||
uses: actions/cache/save@v3 | ||
if: always() | ||
with: | ||
path: gcs_cache | ||
key: gcs_cache_tests_20230811 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters