ENH: Separate workflow for histopathology

.github/workflows/build-test-pr.yml → .github/workflows/hi-ml-pr.yml

@@ -1,11 +1,15 @@
-name: PR BuildAndTest.CI
+name: HI-ML HI-ML-Azure PR
 on:
   push:
     branches: [ main ]
     tags:
       - '*'
   pull_request:
     branches: [ main ]
+    paths:
+      - "hi-ml-azure/**"
+      - "hi-ml/**"
+      - ".github/workflows/hi-ml-pr.yml"
 
 env:
   pythonVersion: 3.7
@@ -18,10 +22,6 @@ env:
   HIML_DIST_ARTIFACT_SUFFIX: '-dist'
   HIML_PACKAGE_NAME_ARTIFACT_SUFFIX: '-package_name'
   HIML_VERSION_ARTIFACT_SUFFIX: '-latest_version'
-  HIML_COV_DOT_ARTIFACT_SUFFIX: '-code_coverage_report_dot'
-  HIML_COV_HTML_ARTIFACT_SUFFIX: '-code_coverage_report_html'
-  HIML_COV_TXT_ARTIFACT_SUFFIX: '-code_coverage_txt'
-  HIML_COV_XML_ARTIFACT_SUFFIX: '-code_coverage_xml'
 
 jobs:
 
@@ -75,7 +75,7 @@ jobs:
     runs-on: ubuntu-18.04
     strategy:
       matrix:
-        folder: [ hi-ml, hi-ml-azure, hi-ml-histopathology ]
+        folder: [ hi-ml, hi-ml-azure ]
       # This will let all parts of the matrix run, to collect as many errors as possible, rather than aborting after first fail
       fail-fast: false
     steps:
@@ -177,7 +177,6 @@ jobs:
 
       - name: Download package artifacts
         id: download
-        if: ${{ matrix.folder != 'hi-ml-histopathology' }}
         uses: ./.github/actions/download_package_artifacts
         with:
           folder: ${{ matrix.folder }}
@@ -187,11 +186,9 @@ jobs:
         run: |
           cd ${{ matrix.folder }}
 
-          if [ ${{ matrix.folder }} != 'hi-ml-histopathology' ]; then
-            make pip_upgrade
-            # Install package
-            pip install ${{ steps.download.outputs.package_filename }}
-          fi
+          make pip_upgrade
+          # Install package
+          pip install ${{ steps.download.outputs.package_filename }}
 
           if [ ${{ matrix.packageName }} == '*.whl' ]; then
             # Set env vars so wheel is sent to azureml as a private package
@@ -210,68 +207,6 @@ jobs:
         with:
             name: ${{ matrix.folder }}
 
-  test-project-folders:
-    runs-on: ubuntu-18.04
-    needs: [ build-python ]
-    strategy:
-      matrix:
-        folder: [ hi-ml-histopathology ]
-        packageName: [ '*.whl' ]
-    steps:
-      - uses: actions/checkout@v2
-        with:
-          lfs: true
-
-      - name: Set up Python ${{ env.pythonVersion }}
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ env.pythonVersion }}
-
-      - name: PIP upgrade
-        run: |
-          cd hi-ml-azure
-          make pip_upgrade
-
-      - name: Download hi-ml-azure
-        id: download_himlazure
-        uses: ./.github/actions/download_package_artifacts
-        with:
-          folder: hi-ml-azure
-          package_type: ${{ matrix.packageName }}
-
-      - name: Download hi-ml
-        id: download_himl
-        uses: ./.github/actions/download_package_artifacts
-        with:
-          folder: hi-ml
-          package_type: ${{ matrix.packageName }}
-
-      - name: Install dependencies
-        run: |
-          cd hi-ml-azure
-          pip install ${{ steps.download_himlazure.outputs.package_filename }}
-          cd ../hi-ml
-          pip install ${{ steps.download_himl.outputs.package_filename }}
-
-      - name: Run tests
-        run: |
-          cd ${{ matrix.folder }}
-          make pip_local
-          make pytest_and_coverage
-
-      - name: Upload coverage report to Codecov
-        if: ${{ matrix.packageName == '*.whl' }}
-        uses: codecov/codecov-action@v2
-        with:
-            name: ${{ matrix.folder }}
-
-      - name: Run GPU tests
-        run: |
-          branch_prefix="refs/heads/"
-          full_branch_name=$GITHUB_REF
-          branch_name_without_prefix=${full_branch_name#$branch_prefix}
-          python hi-ml-azure/run_pytest.py --mark=gpu --cluster=pr-gpu --conda_env=${{ matrix.folder }}/environment.yml --folder=${{ matrix.folder }} --experiment="$branch_name_without_prefix"
-
   publish-testpypi-pkg:
     runs-on: ubuntu-18.04
     needs: [ test-artifact-pkg ]

.github/workflows/histopathology-pr.yml

@@ -0,0 +1,114 @@
+name: Histopathology PR
+on:
+  push:
+    branches: [ main ]
+    tags:
+      - '*'
+  pull_request:
+    branches: [ main ]
+    paths:
+      - "hi-ml-histopathology/**"
+      - ".github/workflows/histopathology-pr.yml"
+      # When the core hi-ml libraries change, test the histo test too, to find problems with backwards compatibility
+      - "hi-ml-azure/**"
+      - "hi-ml/**"
+
+env:
+  pythonVersion: 3.7
+  folder: hi-ml-histopathology
+  HIML_TENANT_ID: ${{ secrets.HIML_TENANT_ID }}
+  HIML_RESOURCE_GROUP: ${{ secrets.HIML_RESOURCE_GROUP }}
+  HIML_SUBSCRIPTION_ID: ${{ secrets.HIML_SUBSCRIPTION_ID }}
+  HIML_WORKSPACE_NAME: ${{ secrets.HIML_WORKSPACE_NAME }}
+  HIML_SERVICE_PRINCIPAL_ID: ${{ secrets.HIML_SERVICE_PRINCIPAL_ID }}
+  HIML_SERVICE_PRINCIPAL_PASSWORD: ${{ secrets.HIML_SERVICE_PRINCIPAL_PASSWORD }}
+
+jobs:
+
+  flake8:
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          lfs: true
+
+      - name: Set up Python ${{ env.pythonVersion }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ env.pythonVersion }}
+
+      - name: flake8
+        run: |
+          cd ${{ env.folder }}
+          make pip_test
+          make flake8
+
+  mypy:
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          lfs: true
+
+      - name: Set up Python ${{ env.pythonVersion }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ env.pythonVersion }}
+
+      - name: mypy
+        run: |
+          cd ${{ env.folder }}
+          make pip_test
+          make mypy
+
+  pytest:
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          lfs: true
+
+      - name: Set up Python ${{ env.pythonVersion }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ env.pythonVersion }}
+
+      - name: PIP upgrade
+        run: |
+          cd ${{ env.folder }}
+          make pip_upgrade
+
+      - name: Install required packages
+        run: |
+          cd ${{ env.folder }}
+          make pip_from_conda
+
+      - name: Install hi-ml locally
+        run: |
+          cd hi-ml
+          make pip_local
+
+      - name: Install hi-ml-azure locally
+        run: |
+          cd hi-ml-azure
+          make pip_local
+
+      - name: Test with pytest
+        run: |
+          cd ${{ env.folder }}
+
+          # Run tests
+          make pip_test
+          make pytest_coverage
+
+      - name: Upload coverage report to Codecov
+        uses: codecov/codecov-action@v2
+        with:
+            name: ${{ env.folder }}
+
+      - name: Run GPU tests
+        run: |
+          branch_prefix="refs/heads/"
+          full_branch_name=$GITHUB_REF
+          branch_name_without_prefix=${full_branch_name#$branch_prefix}
+          python hi-ml-azure/run_pytest.py --mark=gpu --cluster=pr-gpu --conda_env=${{ env.folder }}/environment.yml --folder=${{ env.folder }} --experiment="$branch_name_without_prefix"

.github/workflows/multimodal-pr.yml

@@ -1,4 +1,4 @@
-name: Multimodal PR Workflow
+name: Multimodal PR
 on:
   push:
     branches: [ main ]
@@ -8,6 +8,7 @@ on:
     branches: [ main ]
     paths:
       - "multimodal/**"
+      - ".github/workflows/multimodal-pr.yml"
 
 env:
   pythonVersion: 3.7
@@ -18,13 +19,6 @@ env:
   HIML_WORKSPACE_NAME: ${{ secrets.HIML_WORKSPACE_NAME }}
   HIML_SERVICE_PRINCIPAL_ID: ${{ secrets.HIML_SERVICE_PRINCIPAL_ID }}
   HIML_SERVICE_PRINCIPAL_PASSWORD: ${{ secrets.HIML_SERVICE_PRINCIPAL_PASSWORD }}
-  HIML_DIST_ARTIFACT_SUFFIX: '-dist'
-  HIML_PACKAGE_NAME_ARTIFACT_SUFFIX: '-package_name'
-  HIML_VERSION_ARTIFACT_SUFFIX: '-latest_version'
-  HIML_COV_DOT_ARTIFACT_SUFFIX: '-code_coverage_report_dot'
-  HIML_COV_HTML_ARTIFACT_SUFFIX: '-code_coverage_report_html'
-  HIML_COV_TXT_ARTIFACT_SUFFIX: '-code_coverage_txt'
-  HIML_COV_XML_ARTIFACT_SUFFIX: '-code_coverage_xml'
 
 jobs:
 

Makefile

@@ -8,7 +8,6 @@ env:
 
 # call make for each sub package
 define call_packages
-	cd hi-ml-histopathology && ${MAKE} $(1)
 	cd hi-ml-azure && $(MAKE) $(1)
 	cd hi-ml && $(MAKE) $(1)
 endef

hi-ml-histopathology/Makefile

@@ -3,43 +3,30 @@
 # Create a Conda environment for this folder only
 env:
 	conda env create --file environment.yml
-	pip install -r ../test_requirements.txt
-	pip install -r ../build_requirements.txt
+	pip install -r requirements_test.txt
+	pip install -r requirements_build.txt
 
-# call make for parent
-define call_parent
-	cd .. && $(MAKE) $(1)
-endef
-
-## Package management
+# Package management
 
 # pip upgrade
 pip_upgrade:
-	$(call call_parent,pip_upgrade)
+	python -m pip install --upgrade pip
 
 # pip upgrade and install build requirements
-pip_build:
-	$(call call_parent,pip_build)
+pip_build: pip_upgrade
+	pip install -r requirements_build.txt
 
 # pip upgrade and install test requirements
-pip_test:
-	$(call call_parent,pip_test)
+pip_test: pip_upgrade
+	pip install -r requirements_test.txt
 
 # pip install all requirements for histo, read off the Conda file. This is somewhat hacky,
 # we could also build a full Conda before starting the tests. Unclear about the performance
 # impact of that.
-call_pip_local:
+pip_from_conda:
 	sed -e '1,/pip:/ d' environment.yml | grep -v "#" | cut -d "-" -f 2- > temp_requirements.txt
 	pip install -r temp_requirements.txt
 
-# pip upgrade and install local package in editable mode
-pip_local: pip_upgrade call_pip_local
-
-
-# pip install everything for local development and testing
-pip: pip_build pip_test call_pip_local
-
-## Actions
 # clean build artifacts
 clean:
 	rm -vrf `find . -type d -name __pycache__`
@@ -50,48 +37,23 @@ clean:
 	rm -vf ./coverage ./coverage.txt ./coverage.xml
 
 # run flake8, assuming test requirements already installed
-call_flake8:
+flake8:
 	flake8 --count --statistics .
 
-# pip install test requirements and run flake8
-flake8: pip_test call_flake8
-
 # run mypy, assuming test requirements already installed
-call_mypy:
+mypy:
 	mypy --install-types --non-interactive -p histopathology
 	mypy --install-types --non-interactive -p SSL
 	mypy --install-types --non-interactive -p testhisto
 	mypy --install-types --non-interactive -p testSSL
 
-# pip install test requirements and run mypy
-mypy: pip_test call_mypy
-
 # run basic checks
-call_check: call_flake8 call_mypy
-
-# install test requirements and run basic checks
-check: pip_test call_check
+check: flake8 mypy
 
 # run pytest on package, assuming test requirements already installed
-call_pytest:
-	pytest testhisto testSSL
-
-# install test requirements and run tests
-pytest: pip_test testhisto testSSL
-
-# run pytest fast subset on package, assuming test requirements already installed
-call_pytest_fast:
-	pytest -m fast testhisto testSSL
-
-# install test requirements and run pytest fast subset
-pytest_fast: pip_test call_pytest_fast
+pytest:
+	pytest
 
 # run pytest with coverage on package
-call_pytest_and_coverage:
-	pytest --cov=histopathology  --cov-branch --cov-report=html --cov-report=xml --cov-report=term-missing --cov-config=.coveragerc testhisto
-
-# install test requirements and run pytest coverage
-pytest_and_coverage: pip_test call_pytest_and_coverage
-
-# install test requirements and run all tests
-test_all: pip_test call_flake8 call_mypy call_pytest_and_coverage
+pytest_coverage:
+	pytest --cov=histopathology --cov SSL --cov-branch --cov-report=html --cov-report=xml --cov-report=term-missing --cov-config=.coveragerc

hi-ml-histopathology/pytest.ini

@@ -7,4 +7,4 @@ addopts = --strict-markers
 markers =
     fast: Tests that should run very fast, and can act as smoke tests to see if something goes terribly wrong.
     gpu: Tests that should be executed both on a normal machine and on a machine with 2 GPUs.
-    flaky: Tests will automatically rerun if they fail.
+    flaky: Tests will automatically rerun if they fail.