Merge pull request #55 from HERA-Team/progress

Progress
HERA-Team · May 8, 2023 · 7050d19 · 7050d19
2 parents 58b25a2 + fb8d198
commit 7050d19
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Showing 24 changed files with 311 additions and 212 deletions.
diff --git a/.github/workflows/run_notebooks.yaml b/.github/workflows/run_notebooks.yaml
@@ -15,46 +15,51 @@ jobs:
   notebooks:
     name: Running Docs Notebooks
     runs-on: ubuntu-latest
-    defaults:
-     run:
-       # Adding -l {0} ensures conda can be found properly in each step
-       shell: bash -l {0}
+    # defaults:
+    #  run:
+    #    # Adding -l {0} ensures conda can be found properly in each step
+    #    shell: bash -l {0}
     steps:
       - uses: actions/checkout@main
         with:
           fetch-depth: 1
-
-      - name: Cache conda
-        uses: actions/cache@v2
-        env:
-          # Increase this value to reset cache if ci/test-env.yml has not changed
-          CACHE_NUMBER: 0
+      - uses: mpi4py/setup-mpi@v1
+      - name: Setup Python
+        uses: actions/setup-python@v4
         with:
-          path: ~/conda_pkgs_dir
-          key:
-            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ matrix.python-version }}-${{ hashFiles('ci/test-env.yml', 'setup.cfg') }}
+          python-version: ${{ matrix.python-version }}
 
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2.1.1
-        with:
-          # auto-update-conda: true
-          miniconda-version: "latest"
-          python-version: '3.10'
-          environment-file: ci/notebook-env.yml
-          activate-environment: viscpu
-          channels: conda-forge,defaults
-          channel-priority: strict
-          use-only-tar-bz2: true
+      # - name: Cache conda
+      #   uses: actions/cache@v2
+      #   env:
+      #     # Increase this value to reset cache if ci/test-env.yml has not changed
+      #     CACHE_NUMBER: 0
+      #   with:
+      #     path: ~/conda_pkgs_dir
+      #     key:
+      #       ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ matrix.python-version }}-${{ hashFiles('ci/test-env.yml', 'setup.cfg') }}
 
-      - name: Conda Info
-        run: |
-          conda info -a
-          conda list
+      # - name: Setup Miniconda
+      #   uses: conda-incubator/setup-miniconda@v2.1.1
+      #   with:
+      #     # auto-update-conda: true
+      #     miniconda-version: "latest"
+      #     python-version: '3.10'
+      #     environment-file: ci/notebook-env.yml
+      #     activate-environment: viscpu
+      #     channels: conda-forge,defaults
+      #     channel-priority: strict
+      #     use-only-tar-bz2: true
+
+      # - name: Conda Info
+      #   run: |
+      #     conda info -a
+      #     conda list
 
       - name: Install
         run: |
           echo $(which pip)
-          pip install .[test]
+          pip install .[test] papermill jupyter ipykernel
 
       - name: Install ipykernel
         run: python -m ipykernel install --user --name viscpu --display-name "viscpu"

diff --git a/.github/workflows/test_suite.yaml b/.github/workflows/test_suite.yaml
@@ -12,63 +12,88 @@ on:
       - 'main'
 
 jobs:
-  tests:
+  cpu_tests:
     env:
       ENV_NAME: tests
       PYTHON: ${{ matrix.python-version }}
       OS: ${{ matrix.os }}
+      LOG_LEVEL: ${{ (matrix.os == 'macos-latest' && 'WARNING') || 'INFO' }} # Suppress logging on macOS
     name: Testing
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.8, 3.9, "3.10"]
-    defaults:
-     run:
-       # Adding -l {0} ensures conda can be found properly in each step
-       shell: bash -l {0}
+        python-version: [3.9, "3.10", "3.11"]
     steps:
       - uses: actions/checkout@main
         with:
           fetch-depth: 1
+      - uses: mpi4py/setup-mpi@v1
+      - uses: FedericoCarboni/setup-ffmpeg@v2
 
-      - name: Cache conda
-        uses: actions/cache@v2
-        env:
-          # Increase this value to reset cache if ci/test-env.yml has not changed
-          CACHE_NUMBER: 0
+      - name: Setup Python
+        uses: actions/setup-python@v4
         with:
-          path: ~/conda_pkgs_dir
-          key:
-            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ matrix.python-version }}-${{ hashFiles('ci/test-env.yml', 'setup.cfg') }}
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install
+        run: |
+          pip install .[test]
+
+      - name: Run Tests
+        run: |
+          python -m pytest --ignore tests/test_plot.py --cov=vis_cpu --cov-config=.coveragerc --cov-report xml:./coverage.xml --durations=25 --log-cli-level=${{ env.LOG_LEVEL}}
+
+      - name: Run Plotting Tests
+        if: matrix.python-version != '3.9' || matrix.os == 'macos-latest'
+        run: |
+          python -m pytest tests/test_plot.py --cov=vis_cpu --cov-config=.coveragerc --cov-append --cov-report xml:./coverage.xml --durations=25 --log-cli-level=INFO
 
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2.1.1
+      - name: Upload coverage report
+        uses: codecov/codecov-action@v3.1.3
         with:
-          # auto-update-conda: true
-          miniconda-version: "latest"
-          python-version: ${{ matrix.python-version }}
-          environment-file: ci/test-env.yml
-          activate-environment: tests
-          channels: conda-forge,defaults
-          channel-priority: strict
-          use-only-tar-bz2: true
+          file: ./coverage.xml
+          flags: unittests
+          name: codecov-umbrella
+          fail_ci_if_error: true
 
-      - name: Conda Info
+  gpu_tests:
+    env:
+      ENV_NAME: tests
+      PYTHON: "3.10"
+      OS: Ubuntu
+    name: Self-Hosted Tests (GPU)
+    runs-on: [self-hosted, gpu]
+
+    steps:
+      - name: Add Home to PATH
         run: |
-          conda info -a
-          conda list
-          PYVER=`python -c "import sys; print('{:d}.{:d}'.format(sys.version_info.major, sys.version_info.minor))"`
-          if [[ $PYVER != $PYTHON ]]; then
-            exit 1;
-          fi
+          echo "/home/locoadmin/bin" >> $GITHUB_PATH
+          echo "/usr/local/cuda/bin" >> $GITHUB_PATH
+
+      - uses: actions/checkout@main
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON }}
 
       - name: Install
         run: |
           echo $(which pip)
-          pip install .[test]
+          pip install .[test,gpu]
 
       - name: Run Tests
         run: |
-          python -m pytest --cov=vis_cpu --cov-config=.coveragerc --cov-report xml:./coverage.xml --durations=25
+          python -m pytest -k "gpu" --cov=vis_cpu --cov-config=.coveragerc --cov-report xml:./coverage.xml --durations=25 --log-cli-level=INFO
+
+      - name: Upload coverage report
+        uses: codecov/codecov-action@v3.1.3
+        with:
+          file: ./coverage.xml
+          flags: unittests
+          name: codecov-umbrella
+          fail_ci_if_error: true
diff --git a/.github/workflows/test_suite_gpu.yaml b/.github/workflows/test_suite_gpu.yaml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@ exclude: '^docs/conf.py|^src/vis_cpu/data/'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.3.0
+  rev: v4.4.0
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
@@ -18,7 +18,7 @@ repos:
     args: ['--fix=no']
 
 - repo: https://github.com/PyCQA/flake8
-  rev: 4.0.1
+  rev: 6.0.0
   hooks:
   - id: flake8
     additional_dependencies:
@@ -33,27 +33,27 @@ repos:
       - flake8-print
 
 - repo: https://github.com/psf/black
-  rev: 22.6.0
+  rev: 23.3.0
   hooks:
   - id: black
 
 - repo: https://github.com/pre-commit/pygrep-hooks
-  rev: v1.9.0
+  rev: v1.10.0
   hooks:
     - id: rst-backticks
 
 - repo: https://github.com/PyCQA/isort
-  rev: 5.10.1
+  rev: 5.12.0
   hooks:
   - id: isort
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v2.37.1
+  rev: v3.3.2
   hooks:
   - id: pyupgrade
-    args: [--py38-plus]
+    args: [--py39-plus]
 
 - repo: https://github.com/asottile/setup-cfg-fmt
-  rev: v1.20.2
+  rev: v2.2.0
   hooks:
   - id: setup-cfg-fmt
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -9,12 +9,16 @@ version: 2
 sphinx:
   configuration: docs/conf.py
 
-conda:
-  environment: docs/environment.yaml
+# conda:
+#   environment: docs/environment.yaml
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
 
 python:
-   version: 3.7
    install:
       - method: pip
         path: .
-   system_packages: true
+        extra_requirements:
+           - docs
diff --git a/ci/test-env.yml b/ci/test-env.yml
@@ -3,18 +3,18 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - mpi4py>=3.0,<4  # Required here so that we get
-  - astropy>=4,<5
-  - numpy>=1.20,<2.0
-  - scipy>=1.6,<2.0
-  - pip>=21.1,<22
+  - mpi4py>=3.0
+  - astropy>=4
+  - numpy>=1.20
+  - scipy>=1.6
+  - pip>=21.1
   - pytest>=6.2.4
   - pytest-cov>=2.11.1
-  - matplotlib>=3.3.4,<4
-  - ipython>=7.22,<8
-  - h5py>=3.2,<4
+  - matplotlib>=3.3.4
+  - ipython>=7.22
+  - h5py>=3.2
   - ffmpeg
   - pyuvdata  # For testing when using UVBeam object
   - pip:
-    - pyuvsim[sim]>=1.2,<1.4
-    - pyradiosky>=0.1.1,<0.3
+    - pyuvsim[sim]>=1.2
+    - pyradiosky>=0.1.1
diff --git a/codecov.yml b/codecov.yml
@@ -1,2 +1,4 @@
 fixes:
   - "/home/runner/work/vis_cpu/::"
+codecov:
+ token: f1912835-f0e2-4153-891b-f68eb359207f