Merge pull request #100 from KrishnaswamyLab/dev

fix mendeley link

.github/workflows/deploy.yml

@@ -0,0 +1,44 @@
+name: Publish Python 🐍 distributions 📦 to PyPI
+
+on:
+  push:
+    branches:
+      - 'master'
+      - 'test_deploy'
+    tags:
+      - '*'
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-18.04
+
+    steps:
+    - uses: actions/checkout@master
+
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.7
+
+    - name: Install pypa/build
+      run: |
+        cd Python
+        python -m pip install build --user
+
+    - name: Build a binary wheel and a source tarball
+      run: |
+        python -m build --sdist --wheel --outdir dist/ .
+
+    - name: Publish distribution 📦 to Test PyPI
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        skip_existing: true
+        password: ${{ secrets.test_pypi_password }}
+        repository_url: https://test.pypi.org/legacy/
+
+    - name: Publish distribution 📦 to PyPI
+      if: startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        password: ${{ secrets.pypi_password }}

.github/workflows/run_tests.yml

@@ -0,0 +1,113 @@
+name: Unit Tests
+
+on:
+  push:
+    branches-ignore:
+      - 'test_deploy'
+  pull_request:
+    branches:
+      - '*'
+
+jobs:
+  run_linter:
+    runs-on: ${{ matrix.config.os }}
+    if: "!contains(github.event.head_commit.message, 'ci skip')"
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+        - {name: 'current', os: ubuntu-latest, python: '3.8' }
+
+    steps:
+    - name: Cancel Previous Runs
+      uses: styfle/cancel-workflow-action@0.6.0
+      with:
+        access_token: ${{ github.token }}
+
+    - uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.config.python }}
+
+    - name: Install tools
+      run: |
+        python -m pip install --upgrade "pip<=21.0"
+        pip install --use-deprecated=legacy-resolver -U wheel setuptools
+        pip install --use-deprecated=legacy-resolver -U black flake8
+    - name: Lint with Black
+      run: |
+        cd Python
+        black . --check --diff
+
+    - name: Lint with flake8
+      run: |
+        flake8 phate || true
+
+  run_tester:
+    runs-on: ${{ matrix.config.os }}
+    if: "!contains(github.event.head_commit.message, 'ci skip')"
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+        - {name: 'current', os: ubuntu-latest, python: '3.8' }
+        - {name: 'prev', os: ubuntu-latest, python: '3.7' }
+        - {name: 'old', os: ubuntu-latest, python: '3.6' }
+
+    steps:
+    - name: Cancel Previous Runs
+      uses: styfle/cancel-workflow-action@0.6.0
+      with:
+        access_token: ${{ github.token }}
+
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+
+    - name: Install system dependencies
+      if: runner.os == 'Linux'
+      run: |
+        sudo apt-get update -qq
+        sudo apt-get install -y libhdf5-dev libhdf5-serial-dev pandoc gfortran libblas-dev liblapack-dev libedit-dev llvm-dev libcurl4-openssl-dev ffmpeg
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.config.python }}
+
+    - name: Cache Python packages
+      uses: actions/cache@v2
+      with:
+        path: ${{ env.pythonLocation }}
+        key: ${{runner.os}}-pip-${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}
+        restore-keys: ${{runner.os}}-pip-${{ env.pythonLocation }}-
+
+    - name: Install package & dependencies
+      run: |
+        cd Python
+        python -m pip install --upgrade "pip<=21.0"
+        pip install --use-deprecated=legacy-resolver -U wheel setuptools
+        pip install --use-deprecated=legacy-resolver -U .[test]
+        python -c "import phate"
+
+    - name: Run tests
+      run: |
+        nose2 -vvv
+
+    - name: Coveralls
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        COVERALLS_SERVICE_NAME: github
+      run: |
+        coveralls
+
+    - name: Upload check results on fail
+      if: failure()
+      uses: actions/upload-artifact@master
+      with:
+        name: ${{ matrix.config.name }}_results
+        path: check

Python/phate/cluster.py

@@ -3,6 +3,7 @@
 import numpy as np
 from .phate import PHATE
 
+
 def silhouette_score(phate_op, n_clusters, random_state=None, **kwargs):
     """Compute the Silhouette score on KMeans on the PHATE potential
 
@@ -19,12 +20,15 @@ def silhouette_score(phate_op, n_clusters, random_state=None, **kwargs):
     -------
     score : float
     """
-    cluster_labels = kmeans(phate_op, n_clusters=n_clusters, random_state=random_state, **kwargs)
+    cluster_labels = kmeans(
+        phate_op, n_clusters=n_clusters, random_state=random_state, **kwargs
+    )
     return metrics.silhouette_score(phate_op.diff_potential, cluster_labels)
-
-
 
-def kmeans(phate_op, n_clusters='auto', max_clusters=10, random_state=None, k=None, **kwargs):
+
+def kmeans(
+    phate_op, n_clusters="auto", max_clusters=10, random_state=None, k=None, **kwargs
+):
     """KMeans on the PHATE potential
 
     Clustering on the PHATE operator as introduced in Moon et al.
@@ -55,15 +59,20 @@ def kmeans(phate_op, n_clusters='auto', max_clusters=10, random_state=None, k=No
         )
         n_clusters = k
     if not isinstance(phate_op, PHATE):
-        raise TypeError("Expected phate_op to be of type PHATE. Got {}".format(phate_op))
+        raise TypeError(
+            "Expected phate_op to be of type PHATE. Got {}".format(phate_op)
+        )
     if phate_op.graph is not None:
-        if n_clusters == 'auto':
+        if n_clusters == "auto":
             n_clusters = np.arange(2, max_clusters)
-            silhouette_scores = [silhouette_score(phate_op, k, random_state=random_state, **kwargs) for k in n_clusters]
+            silhouette_scores = [
+                silhouette_score(phate_op, k, random_state=random_state, **kwargs)
+                for k in n_clusters
+            ]
             n_clusters = n_clusters[np.argmax(silhouette_scores)]
-        return cluster.KMeans(n_clusters, random_state=random_state, **kwargs).fit_predict(
-            phate_op.diff_potential
-        )
+        return cluster.KMeans(
+            n_clusters, random_state=random_state, **kwargs
+        ).fit_predict(phate_op.diff_potential)
     else:
         raise exceptions.NotFittedError(
             "This PHATE instance is not fitted yet. Call "

Python/phate/mds.py

@@ -105,7 +105,7 @@ def smacof(
 
     n_components : int, optional (default: 2)
         number of dimensions in which to embed `D`
-        
+
     metric : bool, optional (default: True)
         Use metric MDS. If False, uses non-metric MDS
 

Python/phate/phate.py

@@ -267,7 +267,7 @@ def __init__(
     @property
     def diff_op(self):
         """diff_op :  array-like, shape=[n_samples, n_samples] or [n_landmark, n_landmark]
-            The diffusion operator built from the graph
+        The diffusion operator built from the graph
         """
         if self.graph is not None:
             if isinstance(self.graph, graphtools.graphs.LandmarkGraph):
@@ -794,7 +794,9 @@ def fit(self, X):
 
         if precomputed is None:
             _logger.info(
-                "Running PHATE on {} observations and {} variables.".format(X.shape[0], X.shape[1])
+                "Running PHATE on {} observations and {} variables.".format(
+                    X.shape[0], X.shape[1]
+                )
             )
         else:
             _logger.info(

Python/setup.py

@@ -14,7 +14,7 @@
     "s_gd2>=1.5",
 ]
 
-test_requires = ["nose2", "anndata"]
+test_requires = ["nose2", "anndata", "coverage", "coveralls"]
 
 doc_requires = ["sphinx", "sphinxcontrib-napoleon"]
 

Python/test/test.py

@@ -36,7 +36,7 @@ def test_simple():
     phate_operator = phate.PHATE(knn=15, t=100, verbose=False)
     tree_phate = phate_operator.fit_transform(tree_data)
     assert tree_phate.shape == (tree_data.shape[0], 2)
-    clusters = phate.cluster.kmeans(phate_operator, n_clusters='auto')
+    clusters = phate.cluster.kmeans(phate_operator, n_clusters="auto")
     assert np.issubdtype(clusters.dtype, np.signedinteger)
     assert len(np.unique(clusters)) >= 2
     assert len(clusters.shape) == 1
@@ -57,7 +57,9 @@ def test_simple():
     G = pygsp.graphs.Graph(G.W)
     phate_operator.fit(G)
     phate_operator.fit(anndata.AnnData(tree_data))
-    with assert_raises_message(TypeError, "Expected phate_op to be of type PHATE. Got 1"):
+    with assert_raises_message(
+        TypeError, "Expected phate_op to be of type PHATE. Got 1"
+    ):
         phate.cluster.kmeans(1)
 
 

Python/tutorial/EmbryoidBody.ipynb

@@ -121,8 +121,8 @@
     "if not os.path.isdir(os.path.join(download_path, \"scRNAseq\", \"T0_1A\")):\n",
     "    # need to download the data\n",
     "    scprep.io.download.download_and_extract_zip(\n",
-    "        \"https://data.mendeley.com/datasets/v6n743h5ng\"\n",
-    "        \"/1/files/7489a88f-9ef6-4dff-a8f8-1381d046afe3/scRNAseq.zip?dl=1\",\n",
+    "        \"https://md-datasets-public-files-prod.s3.eu-west-1.amazonaws.com/\"\n",
+    "        \"5739738f-d4dd-49f7-b8d1-5841abdbeb1e\",\n",
     "        download_path)"
    ]
   },
@@ -114793,7 +114793,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,