Merge pull request galaxyproject#18757 from bernt-matthias/topic/cond…

…a-defaults

Remove `defaults` channel for conda usage

.github/workflows/osx_startup.yaml

@@ -49,9 +49,10 @@ jobs:
         with:
           path: .tox
           key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-osx
-      - name: Install miniconda  # use this job to test using Python from a conda environment
+      - name: Install miniforge  # use this job to test using Python from a conda environment
         uses: conda-incubator/setup-miniconda@v3
         with:
+          miniforge-version: latest
           activate-environment: ''
       - name: Restore client cache
         uses: actions/cache@v4

doc/source/admin/dependency_resolvers.rst

@@ -207,7 +207,7 @@ debug
 ensure_channels
     Conda channels to enable by default. See https://conda.io/docs/user-guide/tasks/manage-channels.html for more
     information about channels. This defaults to the value of the global ``conda_ensure_channels`` option or
-    ``iuc,conda-forge,bioconda,defaults`` otherwise.  This order should be consistent with the `Bioconda prescribed
+    ``conda-forge,bioconda`` otherwise.  This order should be consistent with the `Bioconda prescribed
     order <https://github.com/bioconda/bioconda-recipes/blob/master/config.yml>`__ if it includes ``bioconda``.
 
 auto_install

doc/source/admin/galaxy_options.rst

@@ -477,7 +477,7 @@
 :Description:
     conda channels to enable by default
     (https://conda.io/docs/user-guide/tasks/manage-channels.html)
-:Default: ``conda-forge,bioconda,defaults``
+:Default: ``conda-forge,bioconda``
 :Type: str
 
 

lib/galaxy/config/sample/galaxy.yml.sample

@@ -578,7 +578,7 @@ galaxy:
 
   # conda channels to enable by default
   # (https://conda.io/docs/user-guide/tasks/manage-channels.html)
-  #conda_ensure_channels: conda-forge,bioconda,defaults
+  #conda_ensure_channels: conda-forge,bioconda
 
   # Use locally-built conda packages.
   #conda_use_local: false

lib/galaxy/config/schemas/config_schema.yml

@@ -359,7 +359,7 @@ mapping:
 
       conda_ensure_channels:
         type: str
-        default: conda-forge,bioconda,defaults
+        default: conda-forge,bioconda
         required: false
         desc: |
           conda channels to enable by default

lib/galaxy/tool_util/deps/conda_util.py

@@ -60,13 +60,10 @@ def conda_link() -> str:
         else:
             url = "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh"
     else:
-        if sys.maxsize > 2**32:
-            if "arm64" in platform.platform():
-                url = "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh"
-            else:
-                url = "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh"
+        if "arm64" in platform.platform():
+            url = "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh"
         else:
-            url = "https://repo.anaconda.com/miniconda/Miniconda3-4.5.12-Linux-x86.sh"
+            url = "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh"
     return url
 
 
@@ -75,21 +72,12 @@ def find_conda_prefix() -> str:
     for Miniconda installs.
     """
     home = os.path.expanduser("~")
-    miniconda_2_dest = os.path.join(home, "miniconda2")
-    miniconda_3_dest = os.path.join(home, "miniconda3")
-    anaconda_2_dest = os.path.join(home, "anaconda2")
-    anaconda_3_dest = os.path.join(home, "anaconda3")
-    # Prefer miniconda3 install if both available
-    if os.path.exists(miniconda_3_dest):
-        return miniconda_3_dest
-    elif os.path.exists(miniconda_2_dest):
-        return miniconda_2_dest
-    elif os.path.exists(anaconda_3_dest):
-        return anaconda_3_dest
-    elif os.path.exists(anaconda_2_dest):
-        return anaconda_2_dest
-    else:
-        return miniconda_3_dest
+    destinations = ["miniforge3", "miniconda3", "miniconda2", "anaconda3", "anaconda2"]
+    for destination in destinations:
+        destination = os.path.join(home, destination)
+        if os.path.exists(destination):
+            return destination
+    return os.path.join(home, "miniforge3")
 
 
 class CondaContext(installable.InstallableContext):

lib/galaxy/tool_util/deps/resolvers/conda.py

@@ -45,7 +45,7 @@
 DEFAULT_CONDARC_OVERRIDE = "_condarc"
 # Conda channel order from highest to lowest, following the one used in
 # https://github.com/bioconda/bioconda-recipes/blob/master/config.yml
-DEFAULT_ENSURE_CHANNELS = "conda-forge,bioconda,defaults"
+DEFAULT_ENSURE_CHANNELS = "conda-forge,bioconda"
 CONDA_SOURCE_CMD = """[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '{environment_path}')" ] || {{
 MAX_TRIES=3
 COUNT=0