Merge pull request #338 from bioimage-io/ci-env-caching

Ci env caching

Author: FynnBe

.github/workflows/build.yml

@@ -6,11 +6,15 @@ on:
   pull_request:
     branches: [ "**" ]
 
+defaults:
+  run:
+    shell: bash -l {0}
+
 jobs:
   black:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Check files using the black formatter
         uses: rickstaa/action-black@v1
         id: action_black
@@ -28,20 +32,18 @@ jobs:
       matrix:
         python-version: [3.7, 3.8, 3.9]
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Install Conda environment with Micromamba
       uses: mamba-org/provision-with-micromamba@main
       with:
         cache-downloads: true
-        cache-env: false  # debugging: torch does not detect onnxruntime
+        cache-env: true
         environment-file: dev/environment-torch.yaml
         extra-specs: |
           python=${{ matrix.python-version }}
     - name: additional setup
-      shell: bash -l {0}
       run: pip install --no-deps -e .
     - name: pytest-spec-conda
-      shell: bash -l {0}
       run: pytest --disable-pytest-warnings
 
   test-spec-main:
@@ -50,23 +52,21 @@ jobs:
       matrix:
         python-version: [3.7, 3.8, 3.9]
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Install Conda environment with Micromamba
       uses: mamba-org/provision-with-micromamba@main
       with:
         cache-downloads: true
-        cache-env: false  # todo: detect env cache hit and adapt(skip?) additional setup (conda remove?)
+        cache-env: true
         environment-file: dev/environment-torch.yaml
         extra-specs: |
           python=${{ matrix.python-version }}
     - name: additional setup
-      shell: bash -l {0}
       run: |
-        conda remove --yes --force bioimageio.spec
+        conda remove --yes --force bioimageio.spec || true  # allow failure for cached env
         pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io
         pip install --no-deps -e .
     - name: pytest-spec-main
-      shell: bash -l {0}
       run: pytest --disable-pytest-warnings
 
   test-spec-tf:
@@ -75,24 +75,22 @@ jobs:
       matrix:
         python-version: [3.7, 3.8, 3.9]
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Install Conda environment with Micromamba
       uses: mamba-org/provision-with-micromamba@main
       with:
         cache-downloads: true
-        cache-env: false  # todo: detect env cache hit and adapt(skip?) additional setup (conda remove?)
+        cache-env: true
         environment-file: dev/environment-tf.yaml
         channel-priority: flexible
         extra-specs: |
           python=${{ matrix.python-version }}
     - name: additional setup
-      shell: bash -l {0}
       run: |
-        conda remove --yes --force bioimageio.spec
+        conda remove --yes --force bioimageio.spec || true  # allow failure for cached env
         pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io
         pip install --no-deps -e .
     - name: pytest-spec-tf
-      shell: bash -l {0}
       run: pytest --disable-pytest-warnings
 
   test-spec-tf-legacy:
@@ -101,24 +99,22 @@ jobs:
       matrix:
         python-version: [3.7]
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Install Conda environment with Micromamba
       uses: mamba-org/provision-with-micromamba@main
       with:
         cache-downloads: true
-        cache-env: false  # todo: detect env cache hit and adapt(skip?) additional setup (conda remove?)
+        cache-env: true
         environment-file: dev/environment-tf-legacy.yaml
         channel-priority: flexible
         extra-specs: |
           python=${{ matrix.python-version }}
     - name: additional setup
-      shell: bash -l {0}
       run: |
-        conda remove --yes --force bioimageio.spec
+        conda remove --yes --force bioimageio.spec || true  # allow failure for cached env
         pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io
         pip install --no-deps -e .
     - name: pytest-spec-tf-legacy
-      shell: bash -l {0}
       run: pytest --disable-pytest-warnings
 
   conda-build:
@@ -140,6 +136,5 @@ jobs:
         extra-specs: |
           boa
     - name: linux conda build
-      shell: bash -l {0}
       run: |
         conda mambabuild -c conda-forge conda-recipe