Update CI and versions

.github/workflows/build.yml

@@ -17,12 +17,12 @@ jobs:
     steps:
 
     - name: Checkout repo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: "3.12"
 
     - name: Install dependencies
       run: |

.github/workflows/ci.yml

@@ -29,16 +29,16 @@ jobs:
     # Note: This uses Google-style docstring convention
     # Ref: https://google.github.io/styleguide/pyguide.html
     name: Lint
-    runs-on: "ubuntu-22.04"
+    runs-on: "ubuntu-latest"
     steps:
 
     - name: Checkout repo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: "3.12"
 
     - name: Install dependencies
       run: |
@@ -57,35 +57,30 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest", "windows-latest", "macos-latest"]
-        python: [3.7, 3.9]
+        os: ["ubuntu-latest", "windows-latest", "macos-14"]
+        python: ["3.8", "3.12"]
 
     name: Tests (${{ matrix.os }}, Python ${{ matrix.python }})
     runs-on: ${{ matrix.os }}
-
     steps:
       - name: Checkout repo
         uses: actions/checkout@v3
 
-      - name: Setup Micromamba
-        # https://github.com/mamba-org/setup-micromamba
-        # Note: Set channel-priority in .condarc if needed
-        uses: mamba-org/setup-micromamba@v1
+      - name: Setup Conda
+        uses: conda-incubator/setup-miniconda@v3
         with:
+          miniforge-version: latest
+          conda-solver: "libmamba"
           environment-file: environment.yml
-          cache-environment: true
-          cache-environment-key: environment-${{ hashFiles('environment.yml') }}-${{ hashFiles('pyproject.toml') }}
-          init-shell: >-
-            bash
-            powershell
-          post-cleanup: all
+          activate-environment: sleap-io
+          python-version: ${{ matrix.python }}
 
       - name: Print environment info
         shell: bash -l {0}
         run: |
           which python
-          micromamba info
-          micromamba list
+          conda info
+          conda list
           pip freeze
 
       - name: Install graphics dependencies on Ubuntu
@@ -95,21 +90,13 @@ jobs:
         run: |
           sudo apt-get update && sudo apt-get install libglapi-mesa libegl-mesa0 libegl1 libopengl0 libgl1-mesa-glx
 
-      - name: Test with pytest
-        if: ${{ !(startsWith(matrix.os, 'ubuntu') && matrix.python == 3.9) }}
-        shell: bash -l {0}
-        run: |
-          pytest
-
       - name: Test with pytest (with coverage)
-        if: ${{ startsWith(matrix.os, 'ubuntu') && matrix.python == 3.9 }}
         shell: bash -l {0}
         run: |
-          pytest --cov=sleap_io --cov-report=xml tests/
+          pytest --cov=sleap_io --cov-report=xml --durations=-1 tests/
 
       - name: Upload coverage
-        uses: codecov/codecov-action@v3
-        if: ${{ startsWith(matrix.os, 'ubuntu') && matrix.python == 3.9 }}
+        uses: codecov/codecov-action@v4
         with:
           fail_ci_if_error: true
           verbose: false

environment.yml

@@ -2,16 +2,29 @@ name: sleap-io
 
 channels:
   - conda-forge
-  - defaults
 
 dependencies:
-  - python=3.9
-  - ffmpeg
+  - python
+  - ffmpeg<6.1.0
   - imageio
+  - imageio-ffmpeg
+  - av
   - attrs
-  - h5py
+  - pandas
+  - simplejson
+  - h5py>=3.8.0
+  - hdmf
   - numpy
-  - conda-forge::opencv
+  - opencv<4.9.0
+  - pynwb
+  - ndx-pose
+  - pytest
+  - pytest-cov
+  - black
+  - pydocstyle
+  - toml
+  - twine
+  - build
   - pip
   - pip:
     - "--editable=.[dev]"

pyproject.toml

@@ -10,23 +10,25 @@ authors = [
     {name = "Talmo Pereira", email = "talmo@salk.edu"}
 ]
 description="Standalone utilities for working with pose data from SLEAP and other tools."
-requires-python = ">=3.7"
+requires-python = ">=3.8"
 keywords = ["sleap", "pose tracking", "pose estimation", "behavior"]
 license = {text = "BSD-3-Clause"}
 classifiers = [
-    "Programming Language :: Python :: 3.7",
     "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9"
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12"
 ]
 dependencies = [
-    "numpy>=1.19.2",
-    "attrs>=21.2.0",
-    "h5py>=3.1.0",
+    "numpy",
+    "attrs",
+    "h5py>=3.8.0",
     "pynwb",
     "ndx-pose",
     "pandas",
     "simplejson",
-    "imageio>=2.26.0",
+    "imageio",
     "imageio-ffmpeg",
     "av"
 ]