Merge pull request #1128 from minrk/micromamba-usr-local

put micromamba in /usr/local/bin and use mamba for installs

Author: minrk

repo2docker/buildpacks/conda/__init__.py

@@ -56,7 +56,9 @@ def get_build_env(self):
             ("NPM_CONFIG_GLOBALCONFIG", "${NPM_DIR}/npmrc"),
             ("NB_ENVIRONMENT_FILE", self._nb_environment_file),
             ("MAMBA_ROOT_PREFIX", "${CONDA_DIR}"),
-            ("MAMBA_EXE", "/tmp/bin/micromamba"),
+            # this exe should be used for installs after bootstrap with micromamba
+            # switch this to /usr/local/bin/micromamba to use it for all installs
+            ("MAMBA_EXE", "${CONDA_DIR}/bin/mamba"),
         ]
         if self._nb_requirements_file:
             env.append(("NB_REQUIREMENTS_FILE", self._nb_requirements_file))
@@ -334,13 +336,15 @@ def get_env_scripts(self):
         environment_yml = self.binder_path("environment.yml")
         env_prefix = "${KERNEL_PYTHON_PREFIX}" if self.py2 else "${NB_PYTHON_PREFIX}"
         if os.path.exists(environment_yml):
+            # TODO: when using micromamba, we call $MAMBA_EXE install -p ...
+            # whereas mamba/conda need `env update -p ...` when it's an env.yaml file
             scripts.append(
                 (
                     "${NB_USER}",
                     r"""
                 TIMEFORMAT='time: %3R' \
-                bash -c 'time ${{MAMBA_EXE}} install -p {0} -f "{1}" && \
-                time ${{MAMBA_EXE}} clean --all -y && \
+                bash -c 'time ${{MAMBA_EXE}} env update -p {0} --file "{1}" && \
+                time ${{MAMBA_EXE}} clean --all -f -y && \
                 ${{MAMBA_EXE}} list -p {0} \
                 '
                 """.format(
@@ -359,7 +363,7 @@ def get_env_scripts(self):
                     "${NB_USER}",
                     r"""
                 ${{MAMBA_EXE}} install -p {0} r-base{1} r-irkernel=1.2 r-devtools -y && \
-                ${{MAMBA_EXE}} clean --all -y && \
+                ${{MAMBA_EXE}} clean --all -f -y && \
                 ${{MAMBA_EXE}} list -p {0}
                 """.format(
                         env_prefix, r_pin

repo2docker/buildpacks/conda/activate-conda.sh

@@ -1,13 +1,14 @@
 # enable conda and activate the notebook environment
-/tmp/bin/micromamba shell init -s bash -p ${CONDA_DIR}
-export MAMBA_ROOT_PREFIX="/srv/conda"
-CONDA_PROFILE="${CONDA_DIR}/etc/profile.d/mamba.sh"
-test -f $CONDA_PROFILE && . $CONDA_PROFILE
+eval $(micromamba shell hook -s posix -p ${CONDA_DIR})
+for name in conda mamba; do
+    CONDA_PROFILE="${CONDA_DIR}/etc/profile.d/${name}.sh"
+    test -f $CONDA_PROFILE && . $CONDA_PROFILE
+done
 if [[ "${KERNEL_PYTHON_PREFIX}" != "${NB_PYTHON_PREFIX}" ]]; then
     # if the kernel is a separate env, stack them
     # so both are on PATH, notebook first
-    micromamba activate ${KERNEL_PYTHON_PREFIX}
-    micromamba activate --stack ${NB_PYTHON_PREFIX}
+    mamba activate ${KERNEL_PYTHON_PREFIX}
+    mamba activate --stack ${NB_PYTHON_PREFIX}
 
     # even though it's second on $PATH
     # make sure CONDA_DEFAULT_ENV is the *kernel* env
@@ -16,5 +17,5 @@ if [[ "${KERNEL_PYTHON_PREFIX}" != "${NB_PYTHON_PREFIX}" ]]; then
     # which only contains UI when the two are different
     export CONDA_DEFAULT_ENV="${KERNEL_PYTHON_PREFIX}"
 else
-    micromamba activate ${NB_PYTHON_PREFIX}
+    mamba activate ${NB_PYTHON_PREFIX}
 fi

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

@@ -15,13 +15,13 @@ URL="https://anaconda.org/conda-forge/micromamba/${MAMBA_VERSION}/download/linux
 unset HOME
 mkdir -p ${CONDA_DIR}
 
-time wget -qO- ${URL} | tar -xvj bin/micromamba
-chmod 0755 /tmp/bin/micromamba
+export MICROMAMBA_EXE="/usr/local/bin/micromamba"
 
-export MAMBA_ROOT_PREFIX=${CONDA_DIR}
-export MAMBA_EXE="/tmp/bin/micromamba"
+time wget -qO- ${URL} | tar -xvj bin/micromamba
+mv bin/micromamba "$MICROMAMBA_EXE"
+chmod 0755 "$MICROMAMBA_EXE"
 
-eval "$(/tmp/bin/micromamba shell hook -p ${CONDA_DIR} -s posix)"
+eval "$(${MICROMAMBA_EXE} shell hook -p ${CONDA_DIR} -s posix)"
 
 micromamba activate
 
@@ -43,7 +43,7 @@ echo "installing notebook env:"
 cat "${NB_ENVIRONMENT_FILE}"
 
 
-time micromamba create -p ${NB_PYTHON_PREFIX} -f "${NB_ENVIRONMENT_FILE}"
+time ${MAMBA_EXE} create -p ${NB_PYTHON_PREFIX} --file "${NB_ENVIRONMENT_FILE}"
 
 if [[ ! -z "${NB_REQUIREMENTS_FILE:-}" ]]; then
     echo "installing pip requirements"
@@ -60,7 +60,7 @@ if [[ ! -z "${KERNEL_ENVIRONMENT_FILE:-}" ]]; then
     # install kernel env and register kernelspec
     echo "installing kernel env:"
     cat "${KERNEL_ENVIRONMENT_FILE}"
-    time micromamba create -p ${KERNEL_PYTHON_PREFIX} -f "${KERNEL_ENVIRONMENT_FILE}"
+    time ${MAMBA_EXE} create -p ${KERNEL_PYTHON_PREFIX} --file "${KERNEL_ENVIRONMENT_FILE}"
 
     if [[ ! -z "${KERNEL_REQUIREMENTS_FILE:-}" ]]; then
         echo "installing pip requirements for kernel"
@@ -70,18 +70,18 @@ if [[ ! -z "${KERNEL_ENVIRONMENT_FILE:-}" ]]; then
 
     ${KERNEL_PYTHON_PREFIX}/bin/ipython kernel install --prefix "${NB_PYTHON_PREFIX}"
     echo '' > ${KERNEL_PYTHON_PREFIX}/conda-meta/history
-    micromamba list -p ${KERNEL_PYTHON_PREFIX}
+    ${MAMBA_EXE} list -p ${KERNEL_PYTHON_PREFIX}
 fi
 
 # Clean things out!
-time micromamba clean --all -y
+time ${MAMBA_EXE} clean --all -f -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 ${NB_PYTHON_PREFIX}
+${MAMBA_EXE} list -p ${NB_PYTHON_PREFIX}
 
 # Set NPM config
 ${NB_PYTHON_PREFIX}/bin/npm config --global set prefix ${NPM_DIR}

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(["/tmp/bin/micromamba", "--version"]).decode("utf8").strip()
+out = check_output(["micromamba", "--version"]).decode("utf8").strip()
 assert (
     out
     == """micromamba: 0.19.1

tests/conda/simple-py2/verify

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