From 8363695878067812ba96ff9e26381395305f5df1 Mon Sep 17 00:00:00 2001 From: fynnbe Date: Tue, 16 May 2023 10:55:22 +0200 Subject: [PATCH 1/3] "shell: bash -l {0}" for all steps --- .github/workflows/build.yml | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index e2722b8e..b8c002cd 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -6,6 +6,10 @@ on: pull_request: branches: [ "**" ] +defaults: + run: + shell: bash -l {0} + jobs: black: runs-on: ubuntu-latest @@ -38,10 +42,8 @@ jobs: extra-specs: | python=${{ matrix.python-version }} - name: additional setup - shell: bash -l {0} run: pip install --no-deps -e . - name: pytest-spec-conda - shell: bash -l {0} run: pytest --disable-pytest-warnings test-spec-main: @@ -60,13 +62,11 @@ jobs: extra-specs: | python=${{ matrix.python-version }} - name: additional setup - shell: bash -l {0} run: | conda remove --yes --force bioimageio.spec 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: @@ -86,13 +86,11 @@ jobs: extra-specs: | python=${{ matrix.python-version }} - name: additional setup - shell: bash -l {0} run: | conda remove --yes --force bioimageio.spec pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io pip install --no-deps -e . - name: pytest-spec-tf - shell: bash -l {0} run: pytest --disable-pytest-warnings test-spec-tf-legacy: @@ -112,13 +110,11 @@ jobs: extra-specs: | python=${{ matrix.python-version }} - name: additional setup - shell: bash -l {0} run: | conda remove --yes --force bioimageio.spec 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 From f60e0a84dadf5fc3b229bbe6a11ce18834b73541 Mon Sep 17 00:00:00 2001 From: fynnbe Date: Tue, 16 May 2023 11:37:23 +0200 Subject: [PATCH 2/3] allow failure of conda remove for cached env --- .github/workflows/build.yml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index b8c002cd..1b7c8630 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -37,7 +37,7 @@ jobs: 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=${{ matrix.python-version }} @@ -57,13 +57,13 @@ jobs: uses: mamba-org/provision-with-micromamba@main with: cache-downloads: true - cache-env: false # todo: detect env cache hit and adapt(skip?) additional setup (conda remove?) + cache-env: true environment-file: dev/environment-torch.yaml extra-specs: | python=${{ matrix.python-version }} - name: additional setup 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 @@ -80,14 +80,14 @@ jobs: 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=${{ matrix.python-version }} - name: additional setup run: | - conda remove --yes --force bioimageio.spec + conda remove --yes --force bioimageio.spec || true # allow failure for cached env pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io pip install --no-deps -e . - name: pytest-spec-tf @@ -104,14 +104,14 @@ jobs: uses: mamba-org/provision-with-micromamba@main with: cache-downloads: true - cache-env: false # todo: detect env cache hit and adapt(skip?) additional setup (conda remove?) + cache-env: true environment-file: dev/environment-tf-legacy.yaml channel-priority: flexible extra-specs: | python=${{ matrix.python-version }} - name: additional setup 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 From 16d7c0f0959365a7f6ca1cd3aff57921726d4ec2 Mon Sep 17 00:00:00 2001 From: fynnbe Date: Tue, 16 May 2023 13:08:56 +0200 Subject: [PATCH 3/3] bump checkout version just to get a new commit for ci testing --- .github/workflows/build.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 1b7c8630..76a06b5d 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -14,7 +14,7 @@ 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 @@ -32,7 +32,7 @@ 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: @@ -52,7 +52,7 @@ 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: @@ -75,7 +75,7 @@ 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: @@ -99,7 +99,7 @@ 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: