Refactoring to 1.5.1

.github/workflows/build.yaml

@@ -21,9 +21,9 @@ name: build
 on:
   # Triggers the workflow on push or pull request events but only for the master branch
   push:
-    branches: [ master ]
+    branches: [ "master" ]
   pull_request:
-    branches: [ master ]
+    branches: [ "master" ]
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
@@ -33,59 +33,57 @@ jobs:
   # This workflow contains a single job called "build"
   build:
     # The type of runner that the job will run on
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
 
     strategy:
       matrix:
-        python-version: [3.7]
-        # tf-nightly has some pip version conflicts, so can't be installed.
-        # Use only numbered TF as of now.
-        # tf-version: ["2.4.*", "tf-nightly"]
-        tf-version: ["2.4.*"]
+        python-version: [ '3.10' ]
+        # Which tf-version run.
+        tf-version: [ '2.17.0' ]
         # Which set of tests to run.
-        trax-test: ["lib", "research"]
+        trax-test: [ 'lib','research' ]
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install -q -U setuptools numpy
-        python -m pip install flake8 pytest
-        if [[ ${{matrix.tf-version}} == "tf-nightly" ]]; then python -m pip install tf-nightly; else python -m pip install -q "tensorflow=="${{matrix.tf-version}}; fi
-        pip install -e .[tests,t5]
-    # # Lint with flake8
-    # - name: Lint with flake8
-    #   run: |
-    #     # stop the build if there are Python syntax errors or undefined names
-    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    # Test out right now with only testing one directory.
-    - name: Test with pytest
-      run: |
-        TRAX_TEST=" ${{matrix.trax-test}}" ./oss_scripts/oss_tests.sh
-    # The below step just reports the success or failure of tests as a "commit status".
-    # This is needed for copybara integration.
-    - name: Report success or failure as github status
-      if: always()
-      shell: bash
-      run: |
-        status="${{ job.status }}"
-        lowercase_status=$(echo $status | tr '[:upper:]' '[:lower:]')
-        curl -sS --request POST \
-        --url https://api.github.com/repos/${{ github.repository }}/statuses/${{ github.sha }} \
-        --header 'authorization: Bearer ${{ secrets.GITHUB_TOKEN }}' \
-        --header 'content-type: application/json' \
-        --data '{
-            "state": "'$lowercase_status'",
-            "target_url": "https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}",
-            "description": "'$status'",
-            "context": "github-actions/build"
-            }'
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{matrix.python-version}}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{matrix.python-version}}
+          cache: 'pip'
+      - name: Install dependencies
+        env:
+          PIP_DISABLE_PIP_VERSION_CHECK: '1'
+        run: |
+          python -m pip install -U pip
+          # Install TensorFlow matching matrix version.
+          python -m pip install "tensorflow==${{ matrix.tf-version }}"
+          # Install package in editable mode with test and T5 extras (tests use T5 preprocessors).
+          python -m pip install -e .[tests,t5,rl]
+      # Test out right now with only testing one directory.
+      - name: Install trax package
+        run: |
+          python -m pip install -e .
+      - name: Test with pytest
+        working-directory: .
+        run: |
+          TRAX_TEST="${{matrix.trax-test}}" ./oss_scripts/oss_tests.sh
+      # The below step just reports the success or failure of tests as a "commit status".
+      # This is needed for copy bara integration.
+      - name: Report success or failure as github status
+        if: always()
+        shell: bash
+        run: |
+          status="${{ job.status }}"
+          lowercase_status=$(echo $status | tr '[:upper:]' '[:lower:]')
+          curl -sS --request POST \
+          --url https://api.github.com/repos/${{github.repository}}/statuses/${{github.sha}} \
+          --header 'authorization: Bearer ${{ secrets.GITHUB_TOKEN }}' \
+          --header 'content-type: application/json' \
+          --data '{
+              "state": "'$lowercase_status'",
+              "target_url": "https://github.com/${{github.repository}}/actions/runs/${{github.run_id}}",
+              "description": "'$status'",
+              "context": "github-actions/build"
+              }'

.github/workflows/codeql.yml

@@ -0,0 +1,82 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "1.5.1" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "1.5.1" ]
+  schedule:
+    - cron: '31 4 * * 1'
+
+jobs:
+  analyze:
+    name: Analyze
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners
+    # Consider using larger runners for possible analysis time improvements.
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift' ]
+        # Use only 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use only 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+
+    # Autobuild attempts to build any compiled languages (C/C++, C#, Go, Java, or Swift).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v2
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #     echo "Run, Build Application using script"
+    #     ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:${{matrix.language}}"

.readthedocs.yaml

@@ -28,6 +28,6 @@ formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
+  version: 3.10
   install:
     - requirements: docs/requirements.txt

.travis.yml

@@ -5,10 +5,10 @@ git:
   depth: 3
   quiet: true
 python:
-  - "3.6"
+  - "3.10"
 env:
   global:
-    - TF_VERSION="2.4.*"
+    - TF_VERSION="2.11.0"
   matrix:
     - TRAX_TEST="lib"
     - TRAX_TEST="research"

README.md

@@ -5,7 +5,7 @@
 version](https://badge.fury.io/py/trax.svg)](https://badge.fury.io/py/trax)
 [![GitHub
 Issues](https://img.shields.io/github/issues/google/trax.svg)](https://github.com/google/trax/issues)
-![GitHub Build](https://github.com/google/trax/actions/workflows/build.yaml/badge.svg)
+![GitHub Build](https://github.com/mmarcinmichal/trax/actions/workflows/build.yaml/badge.svg)
 [![Contributions
 welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg)](CONTRIBUTING.md)
 [![License](https://img.shields.io/badge/License-Apache%202.0-brightgreen.svg)](https://opensource.org/licenses/Apache-2.0)
@@ -26,6 +26,15 @@ Here are a few example notebooks:-
 * [**trax.data API explained**](https://github.com/google/trax/blob/master/trax/examples/trax_data_Explained.ipynb) : Explains some of the major functions in the `trax.data` API 
 * [**Named Entity Recognition using Reformer**](https://github.com/google/trax/blob/master/trax/examples/NER_using_Reformer.ipynb) : Uses a [Kaggle dataset](https://www.kaggle.com/abhinavwalia95/entity-annotated-corpus) for implementing Named Entity Recognition using the [Reformer](https://arxiv.org/abs/2001.04451) architecture.
 * [**Deep N-Gram models**](https://github.com/google/trax/blob/master/trax/examples/Deep_N_Gram_Models.ipynb) : Implementation of deep n-gram models trained on Shakespeares works
+* **Graph neural networks**: baseline models available via
+  `trax.models.GraphConvNet`,
+  `trax.models.GraphEdgeNet` for node and edge updates, or the
+  attention-based `trax.models.GraphAttentionNet`.
+* Example Python scripts using these GNNs for MNIST and IMDB classification are
+  in
+  [`resources/examples/python/gnn_mnist/train.py`](resources/examples/python/gnn_mnist/train.py)
+  and
+  [`resources/examples/python/gnn_imdb/train.py`](resources/examples/python/gnn_imdb/train.py).
 
 
 

docs/.readthedocs.yaml

@@ -28,6 +28,6 @@ formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
+  version: 3.10
   install:
     - requirements: docs/requirements.txt