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chore!: Remove defaults channel dependency #985

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May 17, 2024
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4 changes: 3 additions & 1 deletion Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -21,10 +21,12 @@ RUN yum install -y mesa-libGL-devel \
# This changes root's .condarc which ENTRYPOINT copies to /home/conda/.condarc later.
RUN . /opt/conda/etc/profile.d/conda.sh && \
conda config \
--add channels defaults \
--add channels bioconda \
--add channels conda-forge \
&& \
conda config \
--remove channels defaults || true \
&& \
{ conda config --remove repodata_fns current_repodata.json 2> /dev/null || true ; } && \
conda config --prepend repodata_fns repodata.json && \
conda config --set channel_priority strict && \
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37 changes: 0 additions & 37 deletions MulledDockerfile

This file was deleted.

4 changes: 0 additions & 4 deletions Mulled_entrypoint

This file was deleted.

2 changes: 1 addition & 1 deletion bioconda_utils/bioconda_utils-conda_build_config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@ numpy:
- 1.21.*

channel_sources:
- conda-forge,bioconda,defaults
- conda-forge,bioconda

channel_targets:
- bioconda main
2 changes: 1 addition & 1 deletion bioconda_utils/pkg_test.py
Original file line number Diff line number Diff line change
Expand Up @@ -95,7 +95,7 @@ def get_image_name(path):
def test_package(
path,
name_override=None,
channels=("conda-forge", "local", "bioconda", "defaults"),
channels=("conda-forge", "local", "bioconda"),
mulled_args="",
base_image=None,
conda_image=MULLED_CONDA_IMAGE,
Expand Down
2 changes: 1 addition & 1 deletion bioconda_utils/utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -1195,7 +1195,7 @@ def get_list(key):

default_config = {
'blacklists': [],
'channels': ['conda-forge', 'bioconda', 'defaults'],
'channels': ['conda-forge', 'bioconda'],
'requirements': None,
'upload_channel': 'bioconda'
}
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1 change: 0 additions & 1 deletion test/test-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,3 @@
channels:
- conda-forge
- bioconda
- defaults
4 changes: 2 additions & 2 deletions test/test_bioconductor_skeleton.py
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@


config = {
'channels': ['conda-forge', 'bioconda', 'defaults']
'channels': ['conda-forge', 'bioconda']
}


Expand Down Expand Up @@ -78,7 +78,7 @@ def test_bioc_write_recipe_no_skipping(tmpdir, bioc_fetch):
@pytest.mark.skip(reason="Does not work since new bioconductor release?")
def test_meta_contents(tmpdir, bioc_fetch):
config = {
'channels': ['conda-forge', 'bioconda', 'defaults']
'channels': ['conda-forge', 'bioconda']
}
bioconductor_skeleton.write_recipe(
'edgeR', recipe_dir=str(tmpdir), config=config, recursive=False, packages=bioc_fetch)
Expand Down