From 9354bb78b257135222460e45387177b25a233103 Mon Sep 17 00:00:00 2001 From: fynnbe Date: Mon, 14 Oct 2024 23:04:51 +0200 Subject: [PATCH 1/5] use collections.abc.Mapping --- bioimageio/core/prediction.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bioimageio/core/prediction.py b/bioimageio/core/prediction.py index 992851f9..6e01d8f4 100644 --- a/bioimageio/core/prediction.py +++ b/bioimageio/core/prediction.py @@ -161,7 +161,7 @@ def predict_many( f"Missing `{{member_id}}` in save_output_path={save_output_path}" ) - if not isinstance(inputs, collections.Mapping) and "{sample_id}" not in str( + if not isinstance(inputs, collections.abc.Mapping) and "{sample_id}" not in str( save_output_path ): raise ValueError( @@ -179,7 +179,7 @@ def predict_many( pp = create_prediction_pipeline(model) - if not isinstance(inputs, collections.Mapping): + if not isinstance(inputs, collections.abc.Mapping): sample_id = str(sample_id) if "{i}" not in sample_id and "{i:" not in sample_id: sample_id += "{i:03}" From 999600b00555db265368151484d5bdd5d191f9f9 Mon Sep 17 00:00:00 2001 From: fynnbe Date: Mon, 14 Oct 2024 23:06:12 +0200 Subject: [PATCH 2/5] bump spec pin --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index a547f780..3ffc8e1f 100644 --- a/setup.py +++ b/setup.py @@ -29,7 +29,7 @@ ], packages=find_namespace_packages(exclude=["tests"]), install_requires=[ - "bioimageio.spec ==0.5.3.2", + "bioimageio.spec ==0.5.3.3", "imageio>=2.10", "loguru", "numpy", From 806e0c1726f9e6bf3df221d82276596d6f6ea0ce Mon Sep 17 00:00:00 2001 From: fynnbe Date: Mon, 14 Oct 2024 23:06:58 +0200 Subject: [PATCH 3/5] bump patch version --- bioimageio/core/VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bioimageio/core/VERSION b/bioimageio/core/VERSION index 8dd7c05c..08e8cc05 100644 --- a/bioimageio/core/VERSION +++ b/bioimageio/core/VERSION @@ -1,3 +1,3 @@ { - "version": "0.6.9" + "version": "0.6.10" } From 390d2a86b49c2d93b63a96c865cacd92457e5572 Mon Sep 17 00:00:00 2001 From: fynnbe Date: Mon, 14 Oct 2024 23:19:56 +0200 Subject: [PATCH 4/5] bump spec in dev envs --- dev/env-py38.yaml | 2 +- dev/env-tf.yaml | 2 +- dev/env-wo-python.yaml | 2 +- dev/env.yaml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/dev/env-py38.yaml b/dev/env-py38.yaml index c96e8f7d..1acb6ec4 100644 --- a/dev/env-py38.yaml +++ b/dev/env-py38.yaml @@ -4,7 +4,7 @@ channels: - conda-forge - defaults dependencies: - - bioimageio.spec>=0.5.3.2 + - bioimageio.spec>=0.5.3.3 - black - crick # uncommented - filelock diff --git a/dev/env-tf.yaml b/dev/env-tf.yaml index 455e9e01..1e0d4dcc 100644 --- a/dev/env-tf.yaml +++ b/dev/env-tf.yaml @@ -4,7 +4,7 @@ channels: - conda-forge - defaults dependencies: - - bioimageio.spec>=0.5.3.2 + - bioimageio.spec>=0.5.3.3 - black # - crick # currently requires python<=3.9 - filelock diff --git a/dev/env-wo-python.yaml b/dev/env-wo-python.yaml index 9a8c2119..26139649 100644 --- a/dev/env-wo-python.yaml +++ b/dev/env-wo-python.yaml @@ -4,7 +4,7 @@ channels: - conda-forge - defaults dependencies: - - bioimageio.spec>=0.5.3.2 + - bioimageio.spec>=0.5.3.3 - black # - crick # currently requires python<=3.9 - filelock diff --git a/dev/env.yaml b/dev/env.yaml index b18482e3..951029ef 100644 --- a/dev/env.yaml +++ b/dev/env.yaml @@ -2,7 +2,7 @@ name: core channels: - conda-forge dependencies: - - bioimageio.spec>=0.5.3.2 + - bioimageio.spec>=0.5.3.3 - black # - crick # currently requires python<=3.9 - filelock From 703d33d51328de704de5243a7613a51863f56c6c Mon Sep 17 00:00:00 2001 From: fynnbe Date: Mon, 14 Oct 2024 23:20:21 +0200 Subject: [PATCH 5/5] split additional setup --- .github/workflows/build.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index addc8fb7..9119a6e9 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -77,11 +77,12 @@ jobs: cache-environment: true environment-file: dev/env-py38.yaml post-cleanup: 'all' - - name: additional setup + - name: additional setup spec run: | 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: additional setup core + run: pip install --no-deps -e . - name: pytest-spec-main run: pytest --disable-pytest-warnings