Fix docker image

Dockerfile

@@ -1,11 +1,26 @@
-FROM mambaorg/micromamba:latest
+FROM mambaorg/micromamba:latest AS mamba_pdal
 COPY environment.yml /environment.yml
 # Using USER root seems to fix permission issues when building mamba environment with pip packages
 USER root
+
+RUN apt update
+RUN apt install -y git
+
 RUN micromamba env create -n patchwork -f /environment.yml
 
-WORKDIR /patchwork
-COPY . /patchwork
+# Start from raw debian image to lower the final image size
+FROM debian:bullseye-slim
+
+# install PDAL + mamba environment
+COPY --from=mamba_pdal /opt/conda/envs/patchwork/bin/pdal /opt/conda/envs/patchwork/bin/pdal
+COPY --from=mamba_pdal /opt/conda/envs/patchwork/bin/python /opt/conda/envs/patchwork/bin/python
+COPY --from=mamba_pdal /opt/conda/envs/patchwork/lib/ /opt/conda/envs/patchwork/lib/
+COPY --from=mamba_pdal /opt/conda/envs/patchwork/ssl /opt/conda/envs/patchwork/ssl
+COPY --from=mamba_pdal /opt/conda/envs/patchwork/share/proj/proj.db /opt/conda/envs/patchwork/share/proj/proj.db
 
 ENV PATH=$PATH:/opt/conda/envs/patchwork/bin/
 ENV PROJ_LIB=/opt/conda/envs/patchwork/share/proj/
+
+WORKDIR /patchwork
+COPY . /patchwork
+

examples/patchwork_example.sh

@@ -0,0 +1,9 @@
+# for selecting, cutting and dispatching lidar files for patchwork
+python main.py \
+    filepath.RECIPIENT_DIRECTORY=[dossier parent du fichier receveur] \
+    filepath.RECIPIENT_NAME=[nom du fichier receveur] \
+    filepath.SHP_DIRECTORY=[dossier parent du shapefile] \
+    filepath.SHP_NAME=[nom du fichier shapefile] \
+    filepath.OUTPUT_DIR=[dossier de sortie] \
+    filepath.OUTPUT_NAME=[nom du fichier de sortie] \
+    \[autres options\]