Merge branch 'master' of github.com:malariagen/malariagen-data-python

malariagen · Sep 5, 2024 · 65fce2c · 65fce2c
2 parents 0570a1b + 27f9589
commit 65fce2c
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diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -16,7 +16,7 @@ jobs:
               uses: actions/checkout@v4
 
             - name: Install poetry
-              run: pipx install poetry==1.8.2
+              run: pipx install poetry==1.8.3
 
             - name: Setup python
               uses: actions/setup-python@v5

diff --git a/.github/workflows/latest_docs.yml b/.github/workflows/latest_docs.yml
@@ -18,7 +18,7 @@ jobs:
           python-version: '3.12'
 
       - name: Install poetry
-        run: pipx install poetry==1.8.2
+        run: pipx install poetry==1.8.3
 
       - name: Eyeball native environment 👀
         run: python --version ; pip --version ; poetry --version ; pwd ; ls -la

diff --git a/.github/workflows/legacy_tests.yml b/.github/workflows/legacy_tests.yml
@@ -7,7 +7,7 @@ on:
     branches:
       - master
 jobs:
-  tests:
+  legacy_tests:
     strategy:
       fail-fast: true
       matrix:
@@ -24,7 +24,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Install poetry
-        run: pipx install poetry==1.8.2
+        run: pipx install poetry==1.8.3
 
       - name: Setup python
         uses: actions/setup-python@v5

diff --git a/.github/workflows/notebooks.yml b/.github/workflows/notebooks.yml
@@ -20,7 +20,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Install poetry
-        run: pipx install poetry==1.8.2
+        run: pipx install poetry==1.8.3
 
       - name: Setup python
         uses: actions/setup-python@v5

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -11,7 +11,7 @@ jobs:
               uses: actions/checkout@v4
 
             - name: Install poetry
-              run: pipx install poetry==1.8.2
+              run: pipx install poetry==1.8.3
 
             - name: Setup python
               uses: actions/setup-python@v5

diff --git a/.github/workflows/tagged_docs.yml b/.github/workflows/tagged_docs.yml
@@ -30,7 +30,7 @@ jobs:
           python-version: '3.12'
 
       - name: Install poetry
-        run: pipx install poetry==1.8.2
+        run: pipx install poetry==1.8.3
 
       - name: Eyeball native environment 👀
         run: python --version ; pip --version ; poetry --version ; pwd ; ls -la

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -11,24 +11,26 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
+        numpy-version:
+          - "numpy==1.26.4"  # current colab version
+          - "numpy~=2.0"  # 2.0 series
+          # numba (0.60.0) does not yet support numpy 2.1, disable this for now
+          # - "numpy~=2.1"  # 2.1 series
     runs-on: ubuntu-latest
 
     steps:
       - name: Checkout source
         uses: actions/checkout@v4
 
-      - name: Install poetry
-        run: pipx install poetry==1.8.2
-
       - name: Setup python
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: "poetry"
+          cache: "pip"
 
-      - name: Install dependencies
-        run: poetry install
+      - name: Install package
+        run: pip install "${{ matrix.numpy-version }}" .[dev]
 
       - name: Run fast unit tests
-        run: poetry run pytest -v tests/anoph --typeguard-packages=malariagen_data,malariagen_data.anoph
+        run: pytest -v tests/anoph --typeguard-packages=malariagen_data,malariagen_data.anoph
diff --git a/malariagen_data/af1.py b/malariagen_data/af1.py
@@ -8,7 +8,7 @@
 MAJOR_VERSION_NUMBER = 1
 MAJOR_VERSION_PATH = "v1.0"
 CONFIG_PATH = "v1.0-config.json"
-GCS_DEFAULT_URL = "gs://vo_afun_release/"
+GCS_DEFAULT_URL = "gs://vo_afun_release_master_us_central1/"
 GCS_REGION_URLS = {
     "us-central1": "gs://vo_afun_release_master_us_central1",
 }

diff --git a/malariagen_data/ag3.py b/malariagen_data/ag3.py
@@ -13,7 +13,7 @@
 MAJOR_VERSION_NUMBER = 3
 MAJOR_VERSION_PATH = "v3"
 CONFIG_PATH = "v3-config.json"
-GCS_DEFAULT_URL = "gs://vo_agam_release/"
+GCS_DEFAULT_URL = "gs://vo_agam_release_master_us_central1/"
 GCS_REGION_URLS = {
     "us-central1": "gs://vo_agam_release_master_us_central1",
 }