replace mamba & conda with micromamba

docs/source/conf.py

@@ -47,7 +47,7 @@
 
 
 def setup(app):
-    app.add_stylesheet("custom.css")  # may also be a URL
+    app.add_css_file("custom.css")  # may also be a URL
     app.add_config_value(
         "recommonmark_config", {"auto_toc_tree_section": "Contents"}, True
     )

repo2docker/buildpacks/conda/__init__.py

@@ -33,6 +33,8 @@ def get_build_env(self):
         env = super().get_build_env() + [
             ("CONDA_DIR", "${APP_BASE}/conda"),
             ("NB_PYTHON_PREFIX", "${CONDA_DIR}/envs/notebook"),
+            ("MAMBA_ROOT_PREFIX", "${CONDA_DIR}"),
+            ("MAMBA_EXE", "/tmp/bin/micromamba"),
         ]
         if self.py2:
             env.append(("KERNEL_PYTHON_PREFIX", "${CONDA_DIR}/envs/kernel"))
@@ -63,7 +65,7 @@ def get_build_scripts(self):
 
         All scripts here should be independent of contents of the repository.
 
-        This sets up through `install-miniforge.bash` (found in this directory):
+        This sets up through `install-base-env.bash` (found in this directory):
 
         - a directory for the conda environment and its ownership by the
           notebook user
@@ -80,8 +82,8 @@ def get_build_scripts(self):
                 "root",
                 r"""
                 TIMEFORMAT='time: %3R' \
-                bash -c 'time /tmp/install-miniforge.bash' && \
-                rm /tmp/install-miniforge.bash /tmp/environment.yml
+                bash -c 'time /tmp/install-base-env.bash' && \
+                rm /tmp/install-base-env.bash /tmp/environment.yml
                 """,
             )
         ]
@@ -104,7 +106,7 @@ def get_build_script_files(self):
 
         """
         files = {
-            "conda/install-miniforge.bash": "/tmp/install-miniforge.bash",
+            "conda/install-base-env.bash": "/tmp/install-base-env.bash",
             "conda/activate-conda.sh": "/etc/profile.d/activate-conda.sh",
         }
         py_version = self.python_version
@@ -277,9 +279,9 @@ def get_env_scripts(self):
                     "${NB_USER}",
                     r"""
                 TIMEFORMAT='time: %3R' \
-                bash -c 'time mamba env update -p {0} -f "{1}" && \
-                time mamba clean --all -f -y && \
-                mamba list -p {0} \
+                bash -c 'time /tmp/bin/micromamba install -p {0} -f "{1}" && \
+                # time /tmp/bin/micromamba clean --all -y && \
+                /tmp/bin/micromamba list -p {0} \
                 '
                 """.format(
                         env_prefix, environment_yml
@@ -296,9 +298,9 @@ def get_env_scripts(self):
                 (
                     "${NB_USER}",
                     r"""
-                mamba install -p {0} r-base{1} r-irkernel={2} r-devtools -y && \
-                mamba clean --all -f -y && \
-                mamba list -p {0}
+                /tmp/bin/micromamba install -p {0} r-base{1} r-irkernel={2} r-devtools -y && \
+                #  /tmp/bin/micromamba clean --all -f -y && \
+                /tmp/bin/micromamba list -p {0}
                 """.format(
                         env_prefix, r_pin, IRKERNEL_VERSION
                     ),

repo2docker/buildpacks/conda/activate-conda.sh

@@ -1,11 +1,13 @@
 # enable conda and activate the notebook environment
-CONDA_PROFILE="${CONDA_DIR}/etc/profile.d/conda.sh"
+export MAMBA_EXE="/tmp/bin/micromamba"
+export MAMBA_ROOT_PREFIX="/srv/conda"
+CONDA_PROFILE="${CONDA_DIR}/etc/profile.d/mamba.sh"
 test -f $CONDA_PROFILE && . $CONDA_PROFILE
 if [[ "${KERNEL_PYTHON_PREFIX}" != "${NB_PYTHON_PREFIX}" ]]; then
     # if the kernel is a separate env, stack them
     # so both are on PATH, notebook first
-    conda activate ${KERNEL_PYTHON_PREFIX}
-    conda activate --stack ${NB_PYTHON_PREFIX}
+    micromamba activate ${KERNEL_PYTHON_PREFIX}
+    micromamba activate --stack ${NB_PYTHON_PREFIX}
 
     # even though it's second on $PATH
     # make sure CONDA_DEFAULT_ENV is the *kernel* env
@@ -14,5 +16,5 @@ if [[ "${KERNEL_PYTHON_PREFIX}" != "${NB_PYTHON_PREFIX}" ]]; then
     # which only contains UI when the two are different
     export CONDA_DEFAULT_ENV="${KERNEL_PYTHON_PREFIX}"
 else
-    conda activate ${NB_PYTHON_PREFIX}
+    micromamba activate ${NB_PYTHON_PREFIX}
 fi

repo2docker/buildpacks/conda/install-base-env.bash

@@ -0,0 +1,68 @@
+#!/bin/bash
+# This downloads and installs a pinned version of micromamba
+# and sets up the base environment
+set -ex
+
+
+cd $(dirname $0)
+
+URL="https://github.com/mamba-org/boa-forge/releases/download/micromamba-nightly-21.5.31.1722/micromamba-nightly-linux-64"
+
+# make sure we don't do anything funky with user's $HOME
+# since this is run as root
+unset HOME
+mkdir -p ${CONDA_DIR}
+
+time wget ${URL} && mkdir bin && mv micromamba-nightly-linux-64 bin/micromamba
+chmod +x bin/micromamba
+
+export MAMBA_ROOT_PREFIX=${CONDA_DIR}
+export MAMBA_EXE="/tmp/bin/micromamba"
+
+eval "$(./bin/micromamba shell hook -p ${CONDA_DIR} -s posix)"
+./bin/micromamba shell init -s bash -p ${CONDA_DIR}
+
+micromamba activate
+
+export PATH="${PWD}/bin:$PATH"
+
+cat <<EOT >> ${CONDA_DIR}/.condarc
+channels:
+  - conda-forge
+  - defaults
+auto_update_conda: false
+show_channel_urls: true
+update_dependencies: false
+channel_priority: strict
+EOT
+
+echo "installing notebook env:"
+cat /tmp/environment.yml
+time micromamba create -p ${NB_PYTHON_PREFIX} -f /tmp/environment.yml
+
+# empty conda history file,
+# which seems to result in some effective pinning of packages in the initial env,
+# which we don't intend.
+# this file must not be *removed*, however
+echo '' > ${NB_PYTHON_PREFIX}/conda-meta/history
+
+if [[ -f /tmp/kernel-environment.yml ]]; then
+    # install kernel env and register kernelspec
+    echo "installing kernel env:"
+    cat /tmp/kernel-environment.yml
+
+    time micromamba create -p ${KERNEL_PYTHON_PREFIX} -f /tmp/kernel-environment.yml
+    ${KERNEL_PYTHON_PREFIX}/bin/ipython kernel install --prefix "${NB_PYTHON_PREFIX}"
+    echo '' > ${KERNEL_PYTHON_PREFIX}/conda-meta/history
+    micromamba list -p ${KERNEL_PYTHON_PREFIX}
+fi
+
+# Clean things out!
+time micromamba clean --all -y
+
+# Remove the pip cache created as part of installing micromamba
+rm -rf /root/.cache
+
+chown -R $NB_USER:$NB_USER ${CONDA_DIR}
+
+micromamba list -p ${NB_PYTHON_PREFIX}

tests/conda/binder-dir/verify

@@ -4,7 +4,7 @@ from subprocess import check_output
 
 assert sys.version_info[:2] == (3, 5), sys.version
 
-out = check_output(["conda", "--version"]).decode("utf8").strip()
-assert out == "conda 4.9.2", out
+out = check_output(["/tmp/bin/micromamba", "--version"]).decode("utf8").strip()
+assert out == "21.5.31.1722", out
 
 import numpy

tests/conda/default-env/postBuild

@@ -1,5 +1,5 @@
 #!/bin/bash
 # install pytest with conda in the default env (should be $KERNEL_PYTHON_PREFIX)
-conda install -yq pytest
+/tmp/bin/micromamba install -yq pytest -p $KERNEL_PYTHON_PREFIX
 # install there with pip (should be the same)
 pip install there

tests/conda/simple-py2/verify

@@ -14,13 +14,17 @@ assert sorted(specs) == ["python2", "python3"], specs.keys()
 import json
 from subprocess import check_output
 
-envs = json.loads(check_output(["conda", "env", "list", "--json"]).decode("utf8"))
+envs = json.loads(
+    check_output(["/tmp/bin/micromamba", "env", "list", "--json"]).decode("utf8")
+)
 assert envs == {
     "envs": ["/srv/conda", "/srv/conda/envs/kernel", "/srv/conda/envs/notebook"]
 }, envs
 
 pkgs = json.loads(
-    check_output(["conda", "list", "-n", "kernel", "--json"]).decode("utf8")
+    check_output(["/tmp/bin/micromamba", "list", "-n", "kernel", "--json"]).decode(
+        "utf8"
+    )
 )
 pkg_names = [pkg["name"] for pkg in pkgs]
 assert "ipykernel" in pkg_names, pkg_names

tests/pipfile/environment-yml/environment.yml

@@ -1,3 +1,4 @@
 dependencies:
+  - pip
   - pip:
       - pypi-pkg-test