Merge pull request #25 from mfhepp/micromamba2.0.4

Update to 2.0.4, add lock/pinning mechanism

Author: mfhepp

Dockerfile

@@ -1,4 +1,4 @@
-ARG MICROMAMBA_VERSION="2.0.2"
+ARG MICROMAMBA_VERSION="2.0.4"
 ARG ENVIRONMENT_FILE="env.yaml"
 ARG NOTEBOOK_MODE
 # Stage 1

README.md

@@ -20,6 +20,7 @@ Based on [`micromamba-docker`](https://github.com/mamba-org/micromamba-docker) a
     - Adding new kernel capabilities is blocked
 - **Development mode,** in which the local version of the Python code can be run inside the container 
 - **Jupyter Notebook / JupyterLab**: You can also run Jupyter Notebook and JupyterLab inside the isolated container.
+- **Reproducible:** `build.sh` writes a YAML specification including versions for all `conda` and `pip` components, which can be used to reproduce a Python environment.
 
 ## Installation
 
@@ -174,6 +175,15 @@ This can be done with the `-f` (for _force_) option:
 
 Note that this may change the installed versions of Python packages. There is currently no mechanism for pinning the installed versions.
 
+### Building from pinned versions
+
+You can build a Docker image from the `*.yaml.lock` files, which contain the pinned versions of all `conda` and `pip` dependencies with the option `-l`, like so
+
+```bash
+./build.sh -l
+./build.sh -nl dataviz
+```
+
 ## Running the Script with `run_script.sh`
 
 This script starts the code in `main.py` inside a Docker container.

build.sh

@@ -19,6 +19,9 @@ NOTEBOOK_ID="notebook"
 BUILD_NOTEBOOK=""
 DIGEST=""
 ENVIRONMENT_FILE="env.yaml"
+LOCK_SUFFIX=""
+# LOCK_SUFFIX=".lock"
+
 
 usage ()
 {
@@ -27,15 +30,16 @@ usage ()
     printf 'Option(s):\n'
     printf "  -d: development mode (create $USER/$APPLICATION_ID:dev)\n"
     printf '  -f: force fresh build, ignoring cached build stages (will e.g. update Python packages)\n'
-    printf "  -n: Jupyter Notebook mode (create $USER/$NOTEBOOK_ID or $USER/$NOTEBOOK_ID:<env_name>)\n"    
+    printf "  -n: Jupyter Notebook mode (create $USER/$NOTEBOOK_ID or $USER/$NOTEBOOK_ID:<env_name>)\n"
+    printf "  -l: build from <env.yaml.lock> file (pinned dependencies)\n"           
 }
 
 if [[ $1 = "--help" ]]; then
    usage
    exit 0
 fi
 
-while getopts ":dfn" opt; do
+while getopts ":dfnl" opt; do
   case ${opt} in
     d)
       if [ "$APPLICATION_ID" = "$NOTEBOOK_ID" ]; then
@@ -50,6 +54,11 @@ while getopts ":dfn" opt; do
       echo "INFO: Force fresh build, ignoring cached build stages (will update Python packages and Debian packages)"
       PARAMETERS="--no-cache"
       ;;
+    l)
+      echo "INFO: Build from LOCK file with pinned dependencies. Implies -f, ignoring cached build stages"
+      PARAMETERS="--no-cache"
+      LOCK_SUFFIX=".lock"
+      ;;      
     n)
       if [ "$DIGEST" = "dev" ]; then
         echo "ERROR: Incompatible options -d and -n. Aborting."
@@ -69,10 +78,12 @@ done
 # Remove processed arguments
 shift $((OPTIND-1))
 
+ENVIRONMENT_FILE="$ENVIRONMENT_FILE$LOCK_SUFFIX"
+
 if [ $# -eq 0 ]; then
   echo "INFO: Environment file = $ENVIRONMENT_FILE"
 else
-  ENVIRONMENT_FILE="$1.yaml"
+  ENVIRONMENT_FILE="$1.yaml$LOCK_SUFFIX"
   # user:test_app:env-dev
   # user:test_app:env
   # user:notebook:env
@@ -92,14 +103,23 @@ docker build $PARAMETERS \
  --build-arg="ENVIRONMENT_FILE=$ENVIRONMENT_FILE" \
 $BUILD_NOTEBOOK \
  --progress=plain --tag $IMAGE_NAME .
-echo INFO: Writing lock file of installed packages for $ENVIRONMENT_FILE
-docker run \
+# Update lock file if we build from the unpinned environment specification
+if [ -z "$LOCK_SUFFIX" ]; then
+  # Command to run if $LOCK_SUFFIX is empty
+  echo INFO: Writing lock file of installed packages for $ENVIRONMENT_FILE
+  docker run \
     --security-opt seccomp=seccomp-default.json \
     --security-opt=no-new-privileges \
     --read-only --tmpfs /tmp \
     --cap-drop all \
     --rm \
     $IMAGE_NAME \
     micromamba env export -n base > $ENVIRONMENT_FILE.lock
-# --explicit would give more details, but would be less portable
-echo INFO: Build completed.
+  # --explicit would give more details, but would be less portable
+  # Since 2.0.4, pip packages are included
+  # See https://github.com/mamba-org/mamba/issues/2008#issuecomment-2500257976
+else
+  echo "INFO: $ENVIRONMENT_FILE will not be updated"
+fi
+
+echo INFO: Build completed.

dataviz.yaml

@@ -27,4 +27,5 @@ dependencies:
 #  - jupyter_ai
 # PyPi modules
 #  - pip:
+#     - pyserial
 #    - black[jupyter]