From e6519b9151881205ca0561c1b3f66a1ae8e8ca69 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Fri, 13 Sep 2024 14:09:24 +0200
Subject: [PATCH] Unpin `numpy` from dependencies and test multiple versions in
 CI

---
 .github/workflows/test.yml | 51 ++++++++++++++------------------------
 setup.cfg                  |  2 +-
 tests/requirements.txt     |  3 +--
 3 files changed, 20 insertions(+), 36 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 110305a..99b7b4e 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -13,37 +13,20 @@ jobs:
       OS: Linux
     strategy:
       matrix:
-        include:
-        - python-version: "3.7"
-          python-release: v3.7
-          python-impl: CPython
-        - python-version: "3.8"
-          python-release: v3.8
-          python-impl: CPython
-        - python-version: "3.9"
-          python-release: v3.9
-          python-impl: CPython
-        - python-version: "3.10"
-          python-release: v3.10
-          python-impl: CPython
-        - python-version: "3.11"
-          python-release: v3.11
-          python-impl: CPython
-        - python-version: "3.12"
-          python-release: v3.12
-          python-impl: CPython
-        - python-version: pypy-3.7
-          python-release: v3.7
-          python-impl: PyPy
-        - python-version: pypy-3.8
-          python-release: v3.8
-          python-impl: PyPy
-        - python-version: pypy-3.9
-          python-release: v3.9
-          python-impl: PyPy
-        - python-version: pypy-3.10
-          python-release: v3.10
-          python-impl: PyPy
+        python-version:
+          - '3.7'
+          - '3.8'
+          - '3.9'
+          - '3.10'
+          - '3.11'
+          - '3.12'
+          - 'pypy-3.7'
+          - 'pypy-3.8'
+          - 'pypy-3.9'
+          - 'pypy-3.10'
+        numpy-version:
+          - '1.0'
+          - '2.0'
     steps:
     - name: Checkout code
       uses: actions/checkout@v4
@@ -55,14 +38,16 @@ jobs:
       run: python -m pip install -U pip wheel setuptools
     - name: Install CI requirements
       run: python -m pip install -r .github/workflows/requirements.txt
+    - name: Install NumPy ${{ matrix.numpy-version }}
+      run: python -m pip install -U 'numpy ~=${{ matrix.numpy-version }}' --prefer-binary
     - name: Install test requirements
       run: python -m pip install -r tests/requirements.txt --prefer-binary
     - name: Test with coverage
       run: python -m coverage run -m unittest discover -vv
     - name: Upload to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
-        flags: ${{ matrix.python-impl }},${{ matrix.python-release }}
+        flags: ${{ matrix.python-version }}
         name: test-python-${{ matrix.python-version }}
         fail_ci_if_error: true
         token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/setup.cfg b/setup.cfg
index e3d18e6..4ce0fa8 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -44,7 +44,7 @@ test_suite = tests
 include_package_data = true
 setup_requires = setuptools >=46.4
 install_requires =
-    numpy ~=1.0
+    numpy
     importlib-resources >=1.3 ; python_version < '3.9'
 
 [options.package_data]
diff --git a/tests/requirements.txt b/tests/requirements.txt
index 21871b4..e0116bd 100644
--- a/tests/requirements.txt
+++ b/tests/requirements.txt
@@ -1,2 +1 @@
-numpy
-biopython
\ No newline at end of file
+biopython