rm mamba from images

.github/workflows/build-images.yml

@@ -175,23 +175,13 @@ jobs:
       with:
         fetch-depth: 0
 
-    # # Clone bioconda-recipes to use as part of the tests.
-    # - uses: actions/checkout@v4
-    #   with:
-    #     fetch-depth: 0
-    #     repository: bioconda/bioconda-recipes
-    #     path: recipes
-
-    # - name: set path
-    #   run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
-
     - name: Install bioconda-utils
       run: |
         export BIOCONDA_DISABLE_BUILD_PREP=1
         wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh
         bash install-and-set-up-conda.sh
         eval "$(conda shell.bash hook)"
-        mamba create -n bioconda -y --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
+        conda create -n bioconda -y --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
         conda activate bioconda
         python setup.py install
 

bioconda_utils/bioconda_utils-requirements.txt

@@ -12,7 +12,6 @@ conda-libmamba-solver=24.1.*
 conda-build=24.5.*
 conda-index=0.4.*
 conda-package-streaming=0.9.*
-mamba=1.5.*
 boa=0.17.*
 
 argh=0.31.*                   # CLI

images/bioconda-utils-build-env-cos7/Dockerfile

@@ -50,14 +50,14 @@ RUN . /opt/conda/etc/profile.d/conda.sh  && conda activate base && \
     sed -nE \
     '/^conda([><!=~ ].+)?$/p' \
     /opt/bioconda-utils/bioconda_utils-requirements.txt \
-    | xargs -r mamba install --yes && \
+    | xargs -r conda install --yes && \
     # FIXME: "remove truststore" only necessary due to python downgrade.
     #        Updating requirements should fix that.
     #        (Also this removal will break in future.)
-    mamba remove --yes truststore && \
-    mamba install --yes --file /opt/bioconda-utils/bioconda_utils-requirements.txt && \
+    conda remove --yes truststore && \
+    conda install --yes --file /opt/bioconda-utils/bioconda_utils-requirements.txt && \
     pip install --no-deps --find-links /opt/bioconda-utils bioconda_utils && \
-    mamba clean --yes --index --tarballs && \
+    conda clean --yes --index --tarballs && \
     # Find files that are not already in group "lucky" and change their group and mode.
     find /opt/conda \
     \! -group lucky \

images/create-env/Dockerfile

@@ -8,10 +8,9 @@ RUN arch="$( uname -m )" \
     wget --quiet -O ./miniconda.sh \
       "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-${arch}.sh"
 
-# Install exact versions of conda/mamba
+# Install exact versions of condaa
 ARG CONDA_VERSION
-ARG MAMBA_VERSION
-RUN echo -e "$CONDA_VERSION\n$MAMBA_VERSION" > requirements.txt
+RUN echo -e "$CONDA_VERSION" > requirements.txt
 RUN ./install-conda ./requirements.txt /opt/create-env
 
 ARG BUSYBOX_IMAGE

images/create-env/Dockerfile.test

@@ -5,7 +5,6 @@ RUN set -x && \
     CONDA_PKGS_DIRS="/tmp/pkgs" \
       /opt/create-env/env-execute \
         create-env \
-          --conda=mamba \
           /usr/local \
           file findutils grep
 RUN set -x && \
@@ -34,7 +33,6 @@ FROM "${base}" as build_bioconda_package
 RUN set -x && \
     /opt/create-env/env-execute \
       create-env \
-        --conda=mamba \
         --strip-files=\* \
         /usr/local \
         python
@@ -58,7 +56,6 @@ FROM "${base}" as build_conda
 RUN set -x && \
     /opt/create-env/env-execute \
       create-env \
-        --conda=mamba \
         --env-activate-args='--prefix-is-base' \
         --strip-files=\* \
         --remove-paths=\*.a \

images/create-env/install-conda

@@ -29,16 +29,16 @@ miniconda_boostrap_prefix="$( pwd )/miniconda"
   # Only need `strip` executable from binutils. Other binaries from the package
   # and especially the "sysroot" dependency is only bloat for this container
   # image. (NOTE: The binary needs libgcc-ng which is explicitly added later.)
-  mamba create --yes \
+  conda create --yes \
     --prefix="${conda_install_prefix}" \
     --channel=conda-forge \
     binutils
   cp -aL "${conda_install_prefix}/bin/strip" ./strip
   conda run --prefix="${conda_install_prefix}" strip -- ./strip
-  mamba remove --yes --all \
+  conda remove --yes --all \
     --prefix="${conda_install_prefix}"
 
-  mamba create --yes \
+  conda create --yes \
     --prefix="${conda_install_prefix}" \
     --channel=conda-forge \
     \
@@ -116,8 +116,7 @@ conda config \
 #     This is intentional as it speeds up conda startup time.
 conda list --name=base
 conda info --all
-mamba --version
-# Make sure we have the requested conda, mamba versions installed.
+# Make sure we have the requested conda version
 conda list \
   --export '^(conda|mamba)$' \
   | sed -n 's/=[^=]*$//p' \

images/create-env/prepare.sh

@@ -5,7 +5,7 @@ BUILD_ARGS=()
 
 
 
-# Get the exact versions of mamba and conda that were installed in build-env.
+# Get the exact versions of conda that wasinstalled in build-env.
 #
 # If this tag exists on quay.io (that is, this create-env is being built in
 # a subsequent run), then use that. Otherwise, we assume this tag has already
@@ -21,16 +21,10 @@ CONDA_VERSION=$(
         podman run -t $REGISTRY/${BUILD_ENV_IMAGE_NAME}:${BIOCONDA_IMAGE_TAG} \
         bash -c "/opt/conda/bin/conda list --export '^conda$'| sed -n 's/=[^=]*$//p'"
 )
-MAMBA_VERSION=$(
-        podman run -t $REGISTRY/${BUILD_ENV_IMAGE_NAME}:${BIOCONDA_IMAGE_TAG} \
-        bash -c "/opt/conda/bin/conda list --export '^mamba$'| sed -n 's/=[^=]*$//p'"
-)
 # Remove trailing \r with parameter expansion
 export CONDA_VERSION=${CONDA_VERSION%$'\r'}
-export MAMBA_VERSION=${MAMBA_VERSION%$'\r'}
 
 BUILD_ARGS+=("--build-arg=CONDA_VERSION=$CONDA_VERSION")
-BUILD_ARGS+=("--build-arg=MAMBA_VERSION=$MAMBA_VERSION")
 
 # Needs busybox image to copy some items over
 if [ $(tag_exists $BASE_BUSYBOX_IMAGE_NAME $BASE_TAG) ]; then