Release 1.2.1

bainzo · Jun 30, 2020 · 9370cae · 9370cae
2 parents 4b0c25c + df610a9
commit 9370cae
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Showing 74 changed files with 405 additions and 315 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -13,7 +13,17 @@ jobs:
     strategy:
       matrix:
         python-version: [3.6, 3.7, 3.8]
-        os: [ubuntu-latest, windows-latest]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        exclude:
+          # skip Mac OS Python 3.7 and 3.8 to save time
+          - python-version: 3.7
+            os: macos-latest
+          - python-version: 3.8
+            os: macos-latest
+
+          # FIXME #1736: tests on Windows with Python3.8 are very slow, so excluded
+          - python-version: 3.8
+            os: windows-latest
 
     runs-on: ${{ matrix.os }}
 
@@ -31,7 +41,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install .[test,demos]
+          pip install .[test]
 
       - name: List dependency versions
         run: "pip freeze"
@@ -144,9 +154,6 @@ jobs:
           # FIXME #818: datasets can't be downloaded
           # FIXME #819: out-of-memory
           - notebook: "demos/community_detection/attacks_clustering_analysis.ipynb"
-          - notebook: "demos/interpretability/gat-node-link-importance.ipynb"
-          - notebook: "demos/interpretability/gcn-node-link-importance.ipynb"
-          - notebook: "demos/interpretability/gcn-sparse-node-link-importance.ipynb"
           - notebook: "demos/interpretability/hateful-twitters-interpretability.ipynb"
           - notebook: "demos/link-prediction/attri2vec-link-prediction.ipynb"
           - notebook: "demos/node-classification/rgcn-node-classification.ipynb"
@@ -182,20 +189,12 @@ jobs:
           path: ${{ matrix.notebook }}
         if: ${{ always() }}
 
-  validate-notebooks-list:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v2
-      - name: Run check
-        run: python3 scripts/ci/ci_workflow_notebook_list.py
-
   neo4j-notebooks:
     runs-on: ubuntu-latest
 
     strategy:
       matrix:
-        neo4j_version: ["3.5", "4.0"]
+        neo4j_version: ["3.5", "4.0", "4.1"]
 
     env:
       STELLARGRAPH_NEO4J_HOST: localhost
@@ -232,7 +231,7 @@ jobs:
         uses: actions/upload-artifact@v1
         if: always()
         with:
-          name: loading-saving-neo4j.ipynb
+          name: loading-saving-neo4j_neo4j-${{ matrix.neo4j_version }}.ipynb
           path: "demos/basics/loading-saving-neo4j.ipynb"
 
       - name: Run load-cora-into-neo4j.ipynb
@@ -241,7 +240,7 @@ jobs:
         uses: actions/upload-artifact@v1
         if: always()
         with:
-          name: load-cora-into-neo4j.ipynb
+          name: load-cora-into-neo4j_neo4j-${{ matrix.neo4j_version }}.ipynb
           path: "demos/connector/neo4j/load-cora-into-neo4j.ipynb"
 
       - name: Run directed-graphsage-on-cora-neo4j-example.ipynb
@@ -252,7 +251,7 @@ jobs:
         uses: actions/upload-artifact@v1
         if: always()
         with:
-          name: directed-graphsage-on-cora-neo4j-example.ipynb
+          name: directed-graphsage-on-cora-neo4j-example_neo4j-${{ matrix.neo4j_version }}.ipynb
           path: "demos/connector/neo4j/directed-graphsage-on-cora-neo4j-example.ipynb"
 
       - name: Run undirected-graphsage-on-cora-neo4j-example.ipynb
@@ -263,7 +262,7 @@ jobs:
         uses: actions/upload-artifact@v1
         if: always()
         with:
-          name: undirected-graphsage-on-cora-neo4j-example.ipynb
+          name: undirected-graphsage-on-cora-neo4j-example_neo4j-${{ matrix.neo4j_version }}.ipynb
           path: "demos/connector/neo4j/undirected-graphsage-on-cora-neo4j-example.ipynb"
 
       - name: Run cluster-gcn-on-cora-neo4j-example.ipynb
@@ -273,7 +272,7 @@ jobs:
         uses: actions/upload-artifact@v1
         if: always()
         with:
-          name: cluster-gcn-on-cora-neo4j-example.ipynb
+          name: cluster-gcn-on-cora-neo4j-example_neo4j-${{ matrix.neo4j_version }}.ipynb
           path: "demos/connector/neo4j/cluster-gcn-on-cora-neo4j-example.ipynb"
 
       # Clean up
@@ -490,3 +489,37 @@ jobs:
       - name: Checking spelling
         run: make spelling SPHINXOPTS=$sphinx_opts
         working-directory: ./docs
+
+  validate-this-workflow:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Run check
+        run: python3 scripts/ci/validate_ci_workflow.py
+
+  # This jobs only exists to be marked as a "required" check on GitHub, because it only runs if
+  # everything else passes. (The list of checks is validated in the step above.)
+  all-jobs-passed:
+    needs:
+      # MARKER: list of all jobs
+      - build
+      - notebooks
+      - neo4j-notebooks
+      - black
+      - check-linters
+      - copyright
+      - whitespace
+      - conda
+      - check-notebook-format
+      - check-notebook-text
+      - shfmt
+      - dockerfile-format
+      - prettier
+      - check-demo-indexing
+      - check-documentation
+      - validate-this-workflow
+
+    runs-on: ubuntu-latest
+    steps:
+      - run: true # the 'needs' is the real testing here
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,21 @@
 # Change Log
 
+## [1.2.1](https://github.com/stellargraph/stellargraph/tree/v1.2.1)
+
+[Full Changelog](https://github.com/stellargraph/stellargraph/compare/v1.2.0...v1.2.1)
+
+This release is a small bug fix release on top of [1.2.0](https://github.com/stellargraph/stellargraph/releases/tag/v1.2.0).
+
+### Bug fixes and other changes
+
+- Update the URLs of some datasets (`Cora`, `PubMedDiabetes`, `CiteSeer`) for upstream changes [\#1738](https://github.com/stellargraph/stellargraph/pull/1738), [\#1759](https://github.com/stellargraph/stellargraph/pull/1759)
+- Add two missing layers to the `stellargraph.custom_keras_layers` dictionary [\#1757](https://github.com/stellargraph/stellargraph/pull/1757)
+- Experimental changes: rename `RotHEScoring` to `RotHEScore` [\#1756](https://github.com/stellargraph/stellargraph/pull/1756)
+- DevOps:
+  - Automated testing on macOS [\#1752](https://github.com/stellargraph/stellargraph/pull/1752)
+  - Automated testing against Neo4j 4.1, in addition to Neo4j 3.5 and 4.0 [\#1754](https://github.com/stellargraph/stellargraph/pull/1754)
+  - Other CI: [\#1732](https://github.com/stellargraph/stellargraph/pull/1732), [\#1740](https://github.com/stellargraph/stellargraph/pull/1740), [\#1741](https://github.com/stellargraph/stellargraph/pull/1741), [\#1744](https://github.com/stellargraph/stellargraph/pull/1744), [\#1745](https://github.com/stellargraph/stellargraph/pull/1745), [\#1747](https://github.com/stellargraph/stellargraph/pull/1747), [\#1750](https://github.com/stellargraph/stellargraph/pull/1750), [\#1751](https://github.com/stellargraph/stellargraph/pull/1751), [\#1753](https://github.com/stellargraph/stellargraph/pull/1753)
+
 ## [1.2.0](https://github.com/stellargraph/stellargraph/tree/v1.2.0)
 
 [Full Changelog](https://github.com/stellargraph/stellargraph/compare/v1.1.0...v1.2.0)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -68,7 +68,7 @@ StellarGraph considers courtesy and respect for others an essential part of the
 
 #### Continuous Integration (CI)
 
-A pull request can only be merged if it passes tests. StellarGraph uses Buildkite CI to let a computer do the testing, and results are reported directly in each pull request. The full Buildkite pipeline can be viewed at <https://buildkite.com/stellar/stellargraph-public/>.
+A pull request can only be merged if it passes tests. StellarGraph uses GitHub Actions to let a computer do the testing, and results are reported directly in each pull request. The CI configuration is in [the `ci.yml` workflow file](.github/workflows/ci.yml), and full set of workflow runs can be viewed at <https://github.com/stellargraph/stellargraph/actions>.
 
 ### Experimental code
 

diff --git a/README.md b/README.md
@@ -8,8 +8,8 @@
 </p>
 <p align="center">
   <a href="https://github.com/stellargraph/stellargraph/blob/develop/CONTRIBUTING.md" alt="contributions welcome"><img src="https://img.shields.io/badge/contributions-welcome-brightgreen.svg"/></a>
-  <a href="https://buildkite.com/stellar/stellargraph-public?branch=master/" alt="Build status: master"><img src="https://img.shields.io/buildkite/8aa4d147372ccc0153101b50137f5f3439c6038f29b21f78f8/master.svg?label=branch:+master"/></a>
-  <a href="https://buildkite.com/stellar/stellargraph-public?branch=develop/" alt="Build status: develop"><img src="https://img.shields.io/buildkite/8aa4d147372ccc0153101b50137f5f3439c6038f29b21f78f8/develop.svg?label=branch:+develop"/></a>
+  <a href="https://github.com/stellargraph/stellargraph/actions?query=branch%3Amaster" alt="Build status: master"><img src="https://github.com/stellargraph/stellargraph/workflows/CI/badge.svg?branch=master"/></a>
+  <a href="https://github.com/stellargraph/stellargraph/actions?query=branch%3Adevelop" alt="Build status: develop"><img src="https://github.com/stellargraph/stellargraph/workflows/CI/badge.svg?branch=develop"/></a>
   <a href="https://codecov.io/gh/stellargraph/stellargraph"><img src="https://codecov.io/gh/stellargraph/stellargraph/branch/develop/graph/badge.svg" /></a>
   <a href="https://pypi.org/project/stellargraph" alt="pypi downloads"><img alt="pypi downloads" src="https://pepy.tech/badge/stellargraph"></a>
 </p>

diff --git a/RELEASE_PROCEDURE.md b/RELEASE_PROCEDURE.md
@@ -88,7 +88,7 @@
      conda build .
      ```
 
-      NOTE: The Conda package is also built in CI, and uploaded to a Buildkite artifact in the "conda build" stage of the pipeline.  It's possible to download this artifact to be uploaded in the following step, rather than building the conda package locally.
+      NOTE: The Conda package is also built in CI, and uploaded to a GitHub Actions artifact in the "conda build" stage of the pipeline.  It's possible to download this artifact to be uploaded in the following step, rather than building the conda package locally.
 
    - Upload to Anaconda Cloud in the “stellargraph” organization
      ```shell

diff --git a/demos/basics/loading-networkx.ipynb b/demos/basics/loading-networkx.ipynb
@@ -58,7 +58,7 @@
     "# install StellarGraph if running on Google Colab\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "  %pip install -q stellargraph[demos]==1.2.0"
+    "  %pip install -q stellargraph[demos]==1.2.1"
    ]
   },
   {
@@ -76,10 +76,10 @@
     "import stellargraph as sg\n",
     "\n",
     "try:\n",
-    "    sg.utils.validate_notebook_version(\"1.2.0\")\n",
+    "    sg.utils.validate_notebook_version(\"1.2.1\")\n",
     "except AttributeError:\n",
     "    raise ValueError(\n",
-    "        f\"This notebook requires StellarGraph version 1.2.0, but a different version {sg.__version__} is installed.  Please see <https://github.com/stellargraph/stellargraph/issues/1172>.\"\n",
+    "        f\"This notebook requires StellarGraph version 1.2.1, but a different version {sg.__version__} is installed.  Please see <https://github.com/stellargraph/stellargraph/issues/1172>.\"\n",
     "    ) from None"
    ]
   },

diff --git a/demos/basics/loading-numpy.ipynb b/demos/basics/loading-numpy.ipynb
@@ -60,7 +60,7 @@
     "# install StellarGraph if running on Google Colab\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "  %pip install -q stellargraph[demos]==1.2.0"
+    "  %pip install -q stellargraph[demos]==1.2.1"
    ]
   },
   {
@@ -78,10 +78,10 @@
     "import stellargraph as sg\n",
     "\n",
     "try:\n",
-    "    sg.utils.validate_notebook_version(\"1.2.0\")\n",
+    "    sg.utils.validate_notebook_version(\"1.2.1\")\n",
     "except AttributeError:\n",
     "    raise ValueError(\n",
-    "        f\"This notebook requires StellarGraph version 1.2.0, but a different version {sg.__version__} is installed.  Please see <https://github.com/stellargraph/stellargraph/issues/1172>.\"\n",
+    "        f\"This notebook requires StellarGraph version 1.2.1, but a different version {sg.__version__} is installed.  Please see <https://github.com/stellargraph/stellargraph/issues/1172>.\"\n",
     "    ) from None"
    ]
   },

diff --git a/demos/basics/loading-pandas.ipynb b/demos/basics/loading-pandas.ipynb
@@ -67,7 +67,7 @@
     "# install StellarGraph if running on Google Colab\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "  %pip install -q stellargraph[demos]==1.2.0"
+    "  %pip install -q stellargraph[demos]==1.2.1"
    ]
   },
   {
@@ -85,10 +85,10 @@
     "import stellargraph as sg\n",
     "\n",
     "try:\n",
-    "    sg.utils.validate_notebook_version(\"1.2.0\")\n",
+    "    sg.utils.validate_notebook_version(\"1.2.1\")\n",
     "except AttributeError:\n",
     "    raise ValueError(\n",
-    "        f\"This notebook requires StellarGraph version 1.2.0, but a different version {sg.__version__} is installed.  Please see <https://github.com/stellargraph/stellargraph/issues/1172>.\"\n",
+    "        f\"This notebook requires StellarGraph version 1.2.1, but a different version {sg.__version__} is installed.  Please see <https://github.com/stellargraph/stellargraph/issues/1172>.\"\n",
     "    ) from None"
    ]
   },

diff --git a/demos/basics/loading-saving-neo4j.ipynb b/demos/basics/loading-saving-neo4j.ipynb
@@ -62,7 +62,7 @@
     "# install StellarGraph if running on Google Colab\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "  %pip install -q stellargraph[demos]==1.2.0"
+    "  %pip install -q stellargraph[demos]==1.2.1"
    ]
   },
   {
@@ -80,10 +80,10 @@
     "import stellargraph as sg\n",
     "\n",
     "try:\n",
-    "    sg.utils.validate_notebook_version(\"1.2.0\")\n",
+    "    sg.utils.validate_notebook_version(\"1.2.1\")\n",
     "except AttributeError:\n",
     "    raise ValueError(\n",
-    "        f\"This notebook requires StellarGraph version 1.2.0, but a different version {sg.__version__} is installed.  Please see <https://github.com/stellargraph/stellargraph/issues/1172>.\"\n",
+    "        f\"This notebook requires StellarGraph version 1.2.1, but a different version {sg.__version__} is installed.  Please see <https://github.com/stellargraph/stellargraph/issues/1172>.\"\n",
     "    ) from None"
    ]
   },

diff --git a/demos/calibration/calibration-link-prediction.ipynb b/demos/calibration/calibration-link-prediction.ipynb
@@ -59,7 +59,7 @@
     "# install StellarGraph if running on Google Colab\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "  %pip install -q stellargraph[demos]==1.2.0"
+    "  %pip install -q stellargraph[demos]==1.2.1"
    ]
   },
   {
@@ -77,10 +77,10 @@
     "import stellargraph as sg\n",
     "\n",
     "try:\n",
-    "    sg.utils.validate_notebook_version(\"1.2.0\")\n",
+    "    sg.utils.validate_notebook_version(\"1.2.1\")\n",
     "except AttributeError:\n",
     "    raise ValueError(\n",
-    "        f\"This notebook requires StellarGraph version 1.2.0, but a different version {sg.__version__} is installed.  Please see <https://github.com/stellargraph/stellargraph/issues/1172>.\"\n",
+    "        f\"This notebook requires StellarGraph version 1.2.1, but a different version {sg.__version__} is installed.  Please see <https://github.com/stellargraph/stellargraph/issues/1172>.\"\n",
     "    ) from None"
    ]
   },

diff --git a/demos/calibration/calibration-node-classification.ipynb b/demos/calibration/calibration-node-classification.ipynb
@@ -53,7 +53,7 @@
     "# install StellarGraph if running on Google Colab\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "  %pip install -q stellargraph[demos]==1.2.0"
+    "  %pip install -q stellargraph[demos]==1.2.1"
    ]
   },
   {
@@ -71,10 +71,10 @@
     "import stellargraph as sg\n",
     "\n",
     "try:\n",
-    "    sg.utils.validate_notebook_version(\"1.2.0\")\n",
+    "    sg.utils.validate_notebook_version(\"1.2.1\")\n",
     "except AttributeError:\n",
     "    raise ValueError(\n",
-    "        f\"This notebook requires StellarGraph version 1.2.0, but a different version {sg.__version__} is installed.  Please see <https://github.com/stellargraph/stellargraph/issues/1172>.\"\n",
+    "        f\"This notebook requires StellarGraph version 1.2.1, but a different version {sg.__version__} is installed.  Please see <https://github.com/stellargraph/stellargraph/issues/1172>.\"\n",
     "    ) from None"
    ]
   },

diff --git a/demos/community_detection/attacks_clustering_analysis.ipynb b/demos/community_detection/attacks_clustering_analysis.ipynb
@@ -94,7 +94,7 @@
     "# install StellarGraph if running on Google Colab\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "  %pip install -q stellargraph[demos]==1.2.0"
+    "  %pip install -q stellargraph[demos]==1.2.1"
    ]
   },
   {
@@ -112,10 +112,10 @@
     "import stellargraph as sg\n",
     "\n",
     "try:\n",
-    "    sg.utils.validate_notebook_version(\"1.2.0\")\n",
+    "    sg.utils.validate_notebook_version(\"1.2.1\")\n",
     "except AttributeError:\n",
     "    raise ValueError(\n",
-    "        f\"This notebook requires StellarGraph version 1.2.0, but a different version {sg.__version__} is installed.  Please see <https://github.com/stellargraph/stellargraph/issues/1172>.\"\n",
+    "        f\"This notebook requires StellarGraph version 1.2.1, but a different version {sg.__version__} is installed.  Please see <https://github.com/stellargraph/stellargraph/issues/1172>.\"\n",
     "    ) from None"
    ]
   },

diff --git a/demos/connector/neo4j/cluster-gcn-on-cora-neo4j-example.ipynb b/demos/connector/neo4j/cluster-gcn-on-cora-neo4j-example.ipynb
@@ -43,7 +43,7 @@
     "# install StellarGraph if running on Google Colab\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "  %pip install -q stellargraph[demos]==1.2.0"
+    "  %pip install -q stellargraph[demos]==1.2.1"
    ]
   },
   {
@@ -61,10 +61,10 @@
     "import stellargraph as sg\n",
     "\n",
     "try:\n",
-    "    sg.utils.validate_notebook_version(\"1.2.0\")\n",
+    "    sg.utils.validate_notebook_version(\"1.2.1\")\n",
     "except AttributeError:\n",
     "    raise ValueError(\n",
-    "        f\"This notebook requires StellarGraph version 1.2.0, but a different version {sg.__version__} is installed.  Please see <https://github.com/stellargraph/stellargraph/issues/1172>.\"\n",
+    "        f\"This notebook requires StellarGraph version 1.2.1, but a different version {sg.__version__} is installed.  Please see <https://github.com/stellargraph/stellargraph/issues/1172>.\"\n",
     "    ) from None"
    ]
   },

diff --git a/demos/connector/neo4j/directed-graphsage-on-cora-neo4j-example.ipynb b/demos/connector/neo4j/directed-graphsage-on-cora-neo4j-example.ipynb
@@ -42,7 +42,7 @@
     "# install StellarGraph if running on Google Colab\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "  %pip install -q stellargraph[demos]==1.2.0"
+    "  %pip install -q stellargraph[demos]==1.2.1"
    ]
   },
   {
@@ -60,10 +60,10 @@
     "import stellargraph as sg\n",
     "\n",
     "try:\n",
-    "    sg.utils.validate_notebook_version(\"1.2.0\")\n",
+    "    sg.utils.validate_notebook_version(\"1.2.1\")\n",
     "except AttributeError:\n",
     "    raise ValueError(\n",
-    "        f\"This notebook requires StellarGraph version 1.2.0, but a different version {sg.__version__} is installed.  Please see <https://github.com/stellargraph/stellargraph/issues/1172>.\"\n",
+    "        f\"This notebook requires StellarGraph version 1.2.1, but a different version {sg.__version__} is installed.  Please see <https://github.com/stellargraph/stellargraph/issues/1172>.\"\n",
     "    ) from None"
    ]
   },