Merge pull request #55 from WenjieDu/dev

Use setup.cfg to manage dependencies for different usages

.github/workflows/testing_daily.yml

@@ -2,40 +2,48 @@ name: Daily Testing
 
 on:
     schedule:
-        # see https://crontab.guru
-        # Run "At 03:00 on Sunday, Tuesday, Thursday, and Saturday."
-        # - cron: '0 3 * * 0,2,4,6'
-        - cron: '0 3 * * *'
+        # https://crontab.guru. Run everyday at 0:00AM UTC, i.e. 08:00AM Beijing, i.e. 08:00PM Montreal (summer time)
+        - cron: "0 0 * * *"
 
 jobs:
     test:
         runs-on: ${{ matrix.os }}
         defaults:
             run:
-                shell: bash -l {0}
+                shell: bash {0}
         strategy:
             fail-fast: false
             matrix:
                 os: [ubuntu-latest, windows-latest, macOS-latest]
                 python-version: ["3.7", "3.9", "3.10"]
+                torch-version: ["1.13.1"]
 
         steps:
             - uses: actions/checkout@v3
 
-            - uses: actions/setup-python@v4
+            - uses: actions/setup-python@v4.3
               with:
                 python-version: ${{ matrix.python-version }}
+                check-latest: true
+                cache: pip
+                cache-dependency-path: |
+                  setup.cfg
 
-            - name: Install Pytorch
+            - name: Install PyTorch ${{ matrix.torch-version }}+cpu
               # we have to install torch in advance because torch_sparse needs it for compilation,
               # refer to https://github.com/rusty1s/pytorch_sparse/issues/156#issuecomment-1304869772 for details
               run: |
+                  which python
+                  which pip
                   python -m pip install --upgrade pip
-                  pip install torch>=1.10.0
+                  pip install torch==${{ matrix.torch-version }} --extra-index-url https://download.pytorch.org/whl/cpu
+                  python -c "import torch; print('PyTorch:', torch.__version__)"
 
             - name: Install other dependencies
               run: |
-                  pip install -r pypots/tests/environment_for_pip_test.txt
+                  pip install -e ".[optional]" -f "https://data.pyg.org/whl/torch-${{ matrix.torch-version }}+cpu.html"
+                  pip install -e ".[basic]"
+                  pip install -e ".[test]"
 
             - name: Fetch the test environment details
               run: |
@@ -46,8 +54,12 @@ jobs:
               run: |
                   coverage run --source=pypots -m pytest
 
-            - name: Submit the report
-              env:
-                  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+            - name: Generate the LCOV report
               run: |
-                  coveralls --service=github
+                  python -m coverage lcov
+
+            - name: Submit the report
+              uses: coverallsapp/github-action@master
+              with:
+                  github-token: ${{ secrets.GITHUB_TOKEN }}
+                  path-to-lcov: "coverage.lcov"

setup.cfg

@@ -15,4 +15,42 @@
 max-line-length = 120
 extend-ignore =
     # why ignore E203? Refer to https://github.com/PyCQA/pycodestyle/issues/373
-    E203,
+    E203,
+
+
+[options.extras_require]
+# add dependencies for different usages below
+
+# basic dependencies
+basic =
+    numpy>=1.23.3
+    scikit-learn>=0.24.1
+    pandas<2.0.0
+    torch>=1.10.0
+    tensorboard
+    scipy
+    h5py
+    tsdb
+    pycorruptor
+
+# dependencies that are optional
+# torch-geometric are only needed for model Raindrop but its installation takes too much time
+optional =
+    torch-geometric
+    torch-scatter
+    torch-sparse
+
+# dependencies for run all functions and models in PyPOTS =  `basic` dependencies + `optional` dependencies
+full =
+    %(basic)s
+    %(optional)s
+
+# dependencies to run tests
+test =
+    pytest-xdist
+    pytest-cov
+
+# dependencies for development = `full` dependencies + `test` dependencies
+dev =
+    %(full)s
+    %(test)s