From cf9bc17fc3663430419c1471da4043f016e6a3dc Mon Sep 17 00:00:00 2001
From: Luis Pedro Coelho <luis@luispedro.org>
Date: Thu, 14 Oct 2021 12:48:56 +0200
Subject: [PATCH] TST Fix testing & update version matrix

- Use the right version of Python in the conda environment
- Include newer Python & NumPy versions
- Use right shell for tests
---
 .github/workflows/python-package-conda.yml    | 33 ------------
 .../test-python-package-with-conda.yml        | 50 +++++++++++++++++++
 2 files changed, 50 insertions(+), 33 deletions(-)
 delete mode 100644 .github/workflows/python-package-conda.yml
 create mode 100644 .github/workflows/test-python-package-with-conda.yml

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
deleted file mode 100644
index d87206e7..00000000
--- a/.github/workflows/python-package-conda.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-name: Test mahotas
-
-on: [push]
-
-jobs:
-  build-linux:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.5', '3.6', '3.7', '3.8']
-        numpy-version:  ['1.16', '1.17', '1.18', '1.19']
-      max-parallel: 5
-
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-    - name: Install dependencies
-      run: |
-        conda install --name base numpy=${{ matrix.numpy-version }}
-        conda install --file tests-requirements.txt --name base
-    - name: Build
-      run: |
-         make debug
-    - name: Test with pytest
-      run: |
-        pytest -v
diff --git a/.github/workflows/test-python-package-with-conda.yml b/.github/workflows/test-python-package-with-conda.yml
new file mode 100644
index 00000000..d503828b
--- /dev/null
+++ b/.github/workflows/test-python-package-with-conda.yml
@@ -0,0 +1,50 @@
+name: Test mahotas
+
+on: [push]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.6', '3.7', '3.8', '3.9']
+        numpy-version:  ['1.17', '1.18', '1.19', '1.20', '1.21']
+        exclude:
+            # 3.6 is too old for NumPy 1.20/1.21
+            - python-version: '3.6'
+              numpy-version: '1.20'
+            - python-version: '3.6'
+              numpy-version: '1.21'
+
+            # NumPy 1.17/1.18 are too old for Python 3.9
+            - python-version: '3.9'
+              numpy-version: '1.17'
+            - python-version: '3.9'
+              numpy-version: '1.18'
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        activate-environment: mahotas_test_env
+        python-version: ${{ matrix.python-version }}
+        auto-activate-base: false
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        conda install --name mahotas_test_env python=${{ matrix.python-version }} numpy=${{ matrix.numpy-version }}
+        conda install --file tests-requirements.txt --name mahotas_test_env
+    - name: Build
+      shell: bash -l {0}
+      run: |
+         conda activate mahotas_test_env
+         make debug
+    - name: Test with pytest
+      shell: bash -l {0}
+      run: |
+         conda activate mahotas_test_env
+         python -m pytest -v