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Minor Fixes From Testing 1.6 (#8897)
### Description This fixes the install issue in the Docker image seen earlier with MetricsReloaded, and fixes a serialisation issue related to moving from pickle to json for Auto3DSeg. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
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Dockerfile

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@@ -30,8 +30,8 @@ WORKDIR /opt/monai
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COPY requirements.txt requirements-min.txt requirements-dev.txt /tmp/
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RUN cp /tmp/requirements.txt /tmp/req.bak \
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&& awk '!/torch/' /tmp/requirements.txt > /tmp/tmp && mv /tmp/tmp /tmp/requirements.txt \
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&& python -m pip install --upgrade --no-cache-dir pip \
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&& python -m pip install --no-cache-dir -r /tmp/requirements-dev.txt
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&& python -m pip install --upgrade --no-cache-dir --no-build-isolation pip wheel wheel-stub \
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&& python -m pip install --no-cache-dir --no-build-isolation -r /tmp/requirements-dev.txt
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# compile ext and remove temp files
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# TODO: remark for issue [revise the dockerfile #1276](https://github.com/Project-MONAI/MONAI/issues/1276)

monai/apps/auto3dseg/bundle_gen.py

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@@ -72,12 +72,13 @@ class BundleAlgo(Algo):
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"""
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def __init__(self, template_path: PathLike):
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def __init__(self, template_path: PathLike | None = None):
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"""
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Create an Algo instance based on the predefined Algo template.
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Args:
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template_path: path to a folder that contains the algorithm templates.
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template_path: path to a folder that contains the algorithm templates. If this is not provided, it's value
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must be loaded with `load_state_dict`.
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Please check https://github.com/Project-MONAI/research-contributions/tree/main/auto3dseg/algorithm_templates
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"""
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based on which path successfully imports the Algo class.
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"""
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return {
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"template_path": self.template_path,
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"data_stats_files": self.data_stats_files,
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"data_list_file": self.data_list_file,
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"mlflow_tracking_uri": self.mlflow_tracking_uri,

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