chore!: Remove defaults channel dependency (#985)

Formally remove usage/dependency on the `defaults` channel. This has been a ToDo on the backlog for a long time and will result in more consistent and more efficient environment resolutions. --------- Signed-off-by: Marcel Bargull <marcel.bargull@udo.edu>
bioconda · May 17, 2024 · eb043dc · eb043dc
1 parent ea286ec
commit eb043dc
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Showing 8 changed files with 8 additions and 48 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -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 && \

diff --git a/MulledDockerfile b/MulledDockerfile
diff --git a/Mulled_entrypoint b/Mulled_entrypoint
diff --git a/bioconda_utils/bioconda_utils-conda_build_config.yaml b/bioconda_utils/bioconda_utils-conda_build_config.yaml
@@ -55,7 +55,7 @@ numpy:
   - 1.21.*
 
 channel_sources:
-  - conda-forge,bioconda,defaults
+  - conda-forge,bioconda
 
 channel_targets:
   - bioconda main
diff --git a/bioconda_utils/pkg_test.py b/bioconda_utils/pkg_test.py
@@ -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,

diff --git a/bioconda_utils/utils.py b/bioconda_utils/utils.py
@@ -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'
     }

diff --git a/test/test-config.yaml b/test/test-config.yaml
@@ -4,4 +4,3 @@
 channels:
     - conda-forge
     - bioconda
-    - defaults
diff --git a/test/test_bioconductor_skeleton.py b/test/test_bioconductor_skeleton.py
@@ -15,7 +15,7 @@
 
 
 config = {
-    'channels': ['conda-forge', 'bioconda', 'defaults']
+    'channels': ['conda-forge', 'bioconda']
 }
 
 
@@ -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)