Merge pull request #532 from bioimage-io/silence_tqdm

Silence tqdm without removing tqdm as a package

Author: FynnBe

.github/workflows/validate_resources.yaml

@@ -104,10 +104,6 @@ jobs:
           conda-forge::bioimageio.spec
       continue-on-error: true  # we inspect this step's outcome in dynamic_validation.py
       timeout-minutes: 60
-    - name: remove tqdm to avoid spamming logs
-      shell: bash -l {0}
-      run: conda remove --yes --force tqdm
-      continue-on-error: true
     - name: get artifact name wo forward slashes
       id: artifact_name
       run: echo ::set-output name=name::dynamic_validation_artifact_$(echo ${{ matrix.resource_id }}_${{ matrix.version_id }}_${{ matrix.weight_format }} | sed 's#/##g')

scripts/download_documentation.py

@@ -1,7 +1,9 @@
 import warnings
+from functools import partial
 from pathlib import Path
 
 import typer
+from tqdm import tqdm
 
 from bioimageio.spec.shared import resolve_source
 from utils import yaml
@@ -31,7 +33,7 @@ def main(
         else:
             type_ext = "md"
 
-        resolve_source(doc_uri, output=rdf_path.with_name(f"documentation.{type_ext}"))
+        resolve_source(doc_uri, output=rdf_path.with_name(f"documentation.{type_ext}"), pbar=partial(tqdm, disable=True))
 
 
 if __name__ == "__main__":

scripts/dynamic_validation.py

@@ -1,13 +1,17 @@
 import traceback
+from functools import partialmethod
 from pathlib import Path
 from typing import List, Optional
 
 import typer
 from marshmallow import missing
+from tqdm import tqdm
 
 from bioimageio.spec import load_raw_resource_description
 from bioimageio.spec.shared import yaml
 
+tqdm.__init__ = partialmethod(tqdm.__init__, disable=True)  # silence tqdm
+
 
 def test_summary_from_exception(name, exception):
     return dict(

scripts/static_validation.py

@@ -1,5 +1,6 @@
 import shutil
 import warnings
+from functools import partialmethod
 from pathlib import Path
 from typing import Dict, List, Optional, Union
 
@@ -8,6 +9,7 @@
 from marshmallow import missing
 from marshmallow.utils import _Missing
 from packaging.version import Version
+from tqdm import tqdm
 
 from bare_utils import set_gh_actions_outputs
 from bioimageio.spec import load_raw_resource_description, validate
@@ -17,6 +19,8 @@
 from bioimageio.spec.shared.raw_nodes import Dependencies, URI
 from utils import ADJECTIVES, ANIMALS, iterate_over_gh_matrix, split_animal_nickname
 
+tqdm.__init__ = partialmethod(tqdm.__init__, disable=True)  # silence tqdm
+
 
 def get_base_env() -> Dict[str, Union[str, List[Union[str, Dict[str, List[str]]]]]]:
     return {"channels": ["defaults"], "dependencies": ["conda-forge::bioimageio.core"]}

scripts/utils.py

@@ -11,16 +11,15 @@
 import numpy
 import requests
 from marshmallow import missing
-from requests import HTTPError
 from ruamel.yaml import YAML, comments
 
 from bare_utils import DEPLOYED_BASE_URL, GH_API_URL
 from bioimageio.spec import (
     load_raw_resource_description,
     serialize_raw_resource_description_to_dict,
 )
+from bioimageio.spec.collection.v0_2.raw_nodes import Collection
 from bioimageio.spec.collection.v0_2.utils import resolve_collection_entries
-from bioimageio.spec.io_ import serialize_raw_resource_description
 from bioimageio.spec.partner.utils import enrich_partial_rdf_with_imjoy_plugin
 
 
@@ -110,9 +109,6 @@ def iterate_over_gh_matrix(matrix: Union[str, Dict[str, list]]):
 def resolve_partners(
     rdf: dict, *, current_format: str, previous_partner_hashes: Dict[str, str]
 ) -> Tuple[List[dict], List[dict], Dict[str, str], set]:
-    from bioimageio.spec import load_raw_resource_description
-    from bioimageio.spec.collection.v0_2.raw_nodes import Collection
-
     partners = []
     updated_partner_resources = []
     new_partner_hashes = {}
@@ -151,7 +147,7 @@ def resolve_partners(
             )
             try:
                 r.raise_for_status()
-            except HTTPError as e:
+            except requests.HTTPError as e:
                 print(e)
                 continue