Merge branch 'master' into tests/remove-random-from-conda

.azure-pipelines/gpu-benchmark.yml

@@ -36,7 +36,7 @@ jobs:
 
     steps:
       - bash: |
-          python -m pytest benchmarks -v --durations=0
+          python -m pytest tests/benchmarks -v --durations=0
         displayName: 'Testing: benchmarks'
         env:
           PL_RUNNING_BENCHMARKS: 1

.azure-pipelines/gpu-tests.yml

@@ -51,7 +51,7 @@ jobs:
     - bash: |
         python -c "fname = 'requirements/extra.txt' ; lines = [line for line in open(fname).readlines() if 'horovod' not in line] ; open(fname, 'w').writelines(lines)"
         pip install fairscale==0.4.0
-        pip install deepspeed==0.5.4
+        pip install deepspeed==0.5.7
         pip install . --requirement requirements/devel.txt
         pip list
       displayName: 'Install dependencies'
@@ -68,14 +68,14 @@ jobs:
       displayName: 'Get legacy checkpoints'
 
     - bash: |
-        python -m coverage run --source pytorch_lightning -m pytest pytorch_lightning tests -v --junitxml=$(Build.StagingDirectory)/test-results.xml --durations=50
+        python -m coverage run --source pytorch_lightning -m pytest pytorch_lightning tests --ignore tests/benchmarks -v --junitxml=$(Build.StagingDirectory)/test-results.xml --durations=50
       displayName: 'Testing: standard'
 
     - bash: |
-        bash tests/special_tests.sh
+        bash tests/standalone_tests.sh
       env:
         PL_USE_MOCKED_MNIST: "1"
-      displayName: 'Testing: special'
+      displayName: 'Testing: standalone'
 
     - bash: |
         python -m coverage report
@@ -113,5 +113,5 @@ jobs:
       displayName: 'Testing: examples'
 
     - bash: |
-        python -m pytest benchmarks -v --maxfail=2 --durations=0
+        python -m pytest tests/benchmarks -v --maxfail=2 --durations=0
       displayName: 'Testing: benchmarks'

.circleci/config.yml

@@ -5,6 +5,19 @@ orbs:
   go: circleci/go@1.3.0
   codecov: codecov/codecov@1.1.0
 
+trigger:
+  tags:
+    include:
+      - '*'
+  branches:
+    include:
+      - "master"
+      - "release/*"
+      - "refs/tags/*"
+pr:
+  - "master"
+  - "release/*"
+
 # Workflow Steps:
 #  1. Checkout
 #  2. Install GO
@@ -24,10 +37,7 @@ references:
     run:
       name: Make Documentation
       command: |
-        # First run the same pipeline as Read-The-Docs
-        # apt-get update && apt-get install -y cmake
-        # using: https://hub.docker.com/r/readthedocs/build
-        # we need to use py3.7 ot higher becase of an issue with metaclass inheritence
+        # the image uses python 2.7 by default, force a different version
         pyenv global 3.7.3
         python --version
         pip install -r requirements/docs.txt

.github/CODEOWNERS

@@ -52,6 +52,7 @@
 /tests/helpers/boring_model.py          @williamfalcon @tchaton @borda
 
 /.github/CODEOWNERS              @williamfalcon
+/SECURITY.md                     @williamfalcon
 /README.md                       @williamfalcon @edenlightning @borda
 /setup.py                        @williamfalcon @borda
 /pytorch_lightning/__about__.py  @williamfalcon @borda

.github/ISSUE_TEMPLATE/bug_report.md

@@ -16,11 +16,11 @@ assignees: ''
 Please reproduce using the BoringModel!
 
 You can use the following Colab link:
-https://colab.research.google.com/drive/1HvWVVTK8j2Nj52qU4Q4YCyzOm0_aLQF3?usp=sharing
+https://colab.research.google.com/github/PytorchLightning/pytorch-lightning/blob/master/pl_examples/bug_report/bug_report_model.ipynb
 IMPORTANT: has to be public.
 
 or this simple template:
-https://github.com/PyTorchLightning/pytorch-lightning/blob/master/pl_examples/bug_report_model.py
+https://github.com/PyTorchLightning/pytorch-lightning/blob/master/pl_examples/bug_report/bug_report_model.py
 
 If you could not reproduce using the BoringModel and still think there's a bug, please post here
 but remember, bugs with code are fixed faster!
@@ -46,9 +46,9 @@ python collect_env_details.py
 You can also fill out the list below manually.
 -->
 
-- PyTorch Lightning Version (e.g., 1.3.0):
-- PyTorch Version (e.g., 1.8)
-- Python version:
+- PyTorch Lightning Version (e.g., 1.5.0):
+- PyTorch Version (e.g., 1.10):
+- Python version (e.g., 3.9):
 - OS (e.g., Linux):
 - CUDA/cuDNN version:
 - GPU models and configuration:

.github/stale.yml

@@ -8,8 +8,8 @@ issues:
     daysUntilClose: 7
     # Issues with these labels will never be considered stale
     exemptLabels:
-      - p0
-      - p1
+      - "priority: 0"
+      - "priority: 1"
     # Comment to post when marking an issue as stale. Set to `false` to disable
     markComment: >
       This issue has been automatically marked as stale because it hasn't had any recent activity.

.github/workflows/ci_pkg-install.yml

@@ -16,7 +16,7 @@ jobs:
       # max-parallel: 6
       matrix:
         os: [ubuntu-20.04, macOS-10.15, windows-2019]
-        python-version: [3.6, 3.9]
+        python-version: [3.7, 3.9]
 
     steps:
       - uses: actions/checkout@v2
@@ -26,12 +26,11 @@ jobs:
 
       - name: Prepare env
         run: |
-          pip install check-manifest "twine==3.2" setuptools wheel
+          pip install "twine==3.2" setuptools wheel
 
       - name: Create package
         run: |
-          check-manifest
-          # python setup.py check --metadata --strict
+          python setup.py check --metadata --strict
           python setup.py sdist bdist_wheel
 
       - name: Check package

.github/workflows/ci_test-base.yml

@@ -59,7 +59,6 @@ jobs:
 
     - name: Test Package [only]
       run: |
-        # NOTE: run coverage on tests does not propagate failure status for Win, https://github.com/nedbat/coveragepy/issues/1003
         coverage run --source pytorch_lightning -m pytest pytorch_lightning -v --junitxml=junit/test-results-${{ runner.os }}-${{ matrix.python-version }}-${{ matrix.requires }}.xml
 
     - name: Upload pytest test results

.github/workflows/ci_test-conda.yml

@@ -17,8 +17,7 @@ jobs:
         python-version: ["3.8"]  # previous to last Python version as that one is already used in test-full
         pytorch-version: ["1.7", "1.8", "1.9", "1.10"]  # nightly: add when there's a release candidate
 
-    # FIXME: undo this before merge
-    timeout-minutes: 75
+    timeout-minutes: 30
     steps:
     - uses: actions/checkout@v2
 
@@ -30,6 +29,8 @@ jobs:
         python ./requirements/adjust_versions.py requirements/extra.txt
         python ./requirements/adjust_versions.py requirements/examples.txt
         pip install --requirement requirements/devel.txt --find-links https://download.pytorch.org/whl/nightly/torch_nightly.html
+        # set a per-test timeout of 2.5 minutes to fail sooner. this aids with hanging tests
+        pip install pytest-timeout
         pip list
 
     - name: Pull checkpoints from S3
@@ -42,8 +43,7 @@ jobs:
 
     - name: Tests
       run: |
-        # NOTE: run coverage on tests does not propagate failure status for Win, https://github.com/nedbat/coveragepy/issues/1003
-        coverage run --source pytorch_lightning -m pytest pytorch_lightning tests -v --durations=50 --junitxml=junit/test-results-${{ runner.os }}-torch${{ matrix.pytorch-version }}.xml
+        coverage run --source pytorch_lightning -m pytest --timeout 150 pytorch_lightning tests -v --durations=50 --junitxml=junit/test-results-${{ runner.os }}-torch${{ matrix.pytorch-version }}.xml
       shell: bash -l {0}
 
     - name: Upload pytest results

.github/workflows/ci_test-full.yml

@@ -21,11 +21,7 @@ jobs:
         python-version: ["3.7", "3.9"]  # minimum, maximum
         requires: ["oldest", "latest"]
         release: ["stable"]
-        include:
-          # test 3.6 only on oldest until EOL: https://github.com/PyTorchLightning/pytorch-lightning/issues/9981
-          - {os: ubuntu-18.04, python-version: "3.6", requires: "oldest", release: "stable"}
-          - {os: windows-2019, python-version: "3.6", requires: "oldest", release: "stable"}
-          - {os: macOS-10.15, python-version: "3.6", requires: "oldest", release: "stable"}
+        #include:
           # nightly: add when there's a release candidate
           #- {os: ubuntu-20.04, python-version: "3.10", requires: "latest", release: "pre"}
 

.github/workflows/ci_test-slow.yml

@@ -0,0 +1,83 @@
+name: Test
+
+# see: https://help.github.com/en/actions/reference/events-that-trigger-workflows
+on:  # Trigger the workflow on push or pull request, but only for the master branch
+  push:
+    branches: [master, "release/*"]
+  pull_request:
+    branches: [master, "release/*"]
+
+jobs:
+  slow:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macOS-latest]
+        # same config as '.azure-pipelines/gpu-tests.yml'
+        python-version: ["3.7"]
+        pytorch-version: ["1.8"]
+
+    timeout-minutes: 20
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Weekly reset caching
+      run: echo "::set-output name=period::$(python -c 'import time ; days = time.time() / 60 / 60 / 24 ; print(int(days / 7))' 2>&1)"
+      id: times
+
+    - name: Get pip cache
+      id: pip-cache
+      run: |
+        python -c "from pip._internal.locations import USER_CACHE_DIR; print('::set-output name=dir::' + USER_CACHE_DIR)"
+
+    - name: Cache pip
+      uses: actions/cache@v2
+      with:
+        path: ${{ steps.pip-cache.outputs.dir }}
+        key: ${{ runner.os }}-pip-td${{ steps.times.outputs.period }}-py${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-td${{ steps.times.outputs.period }}-py${{ matrix.python-version }}-
+
+    - name: Install dependencies
+      run: |
+        # adjust versions according installed Torch version
+        python ./requirements/adjust_versions.py requirements.txt ${{ matrix.pytorch-version }}
+        pip install --requirement requirements.txt --find-links https://download.pytorch.org/whl/cpu/torch_stable.html --upgrade
+        pip install --requirement requirements/test.txt
+        pip list
+      shell: bash
+
+    - name: Tests
+      run: |
+        coverage run --source pytorch_lightning -m pytest tests -v --junitxml=junit/test-results-${{ runner.os }}-${{ matrix.python-version }}.xml
+      env:
+        PL_RUN_SLOW_TESTS: 1
+
+    - name: Upload pytest test results
+      uses: actions/upload-artifact@v2
+      with:
+        name: pytest-results-${{ runner.os }}-${{ matrix.python-version }}
+        path: junit/test-results-${{ runner.os }}-${{ matrix.python-version }}.xml
+      if: failure()
+
+    - name: Statistics
+      if: success()
+      run: |
+        coverage report
+        coverage xml
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1
+      if: success()
+      # see: https://github.com/actions/toolkit/issues/399
+      continue-on-error: true
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: coverage.xml
+        flags: cpu,pytest,torch${{ matrix.pytorch-version }}
+        name: CPU-coverage
+        fail_ci_if_error: false

.github/workflows/code-checks.yml

@@ -14,8 +14,8 @@ jobs:
       - uses: actions/setup-python@v2
         with:
           python-version: 3.9
-      - name: Install mypy
+      - name: Install dependencies
         run: |
-          grep mypy requirements/test.txt | xargs -0 pip install
+          pip install '.[dev]'
           pip list
       - run: mypy --install-types --non-interactive

.github/workflows/release-docker.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python_version: ["3.6", "3.7", "3.8", "3.9"]
+        python_version: ["3.7", "3.8", "3.9"]
         pytorch_version: ["1.7", "1.8", "1.9", "1.10"]
     steps:
       - name: Checkout

.pre-commit-config.yaml

@@ -49,7 +49,7 @@ repos:
     rev: v2.29.0
     hooks:
       - id: pyupgrade
-        args: [--py36-plus]
+        args: [--py37-plus]
         name: Upgrade code
 
   - repo: https://github.com/myint/docformatter
@@ -80,8 +80,8 @@ repos:
     rev: v1.11.0
     hooks:
       - id: blacken-docs
-        args: [ --line-length=120 ]
-        additional_dependencies: [ black==21.7b0 ]
+        args: [--line-length=120]
+        additional_dependencies: [black==21.7b0]
 
   - repo: https://github.com/executablebooks/mdformat
     rev: 0.7.10

.readthedocs.yml

@@ -38,9 +38,17 @@ formats:
   - htmlzip
   #- pdf
 
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+  apt_packages:
+    - texlive-latex-extra
+    - dvipng
+    - texlive-pictures
+
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
   install:
     - requirements: requirements/docs.txt
     #- requirements: requirements.txt