Python conda runner (#210)

* added a first python env at the bottom of the script

* re-ordered

* random change to test build

* edited ref to previous action

* it's not reserved to main branch anymore...

* this should help with matplotlib issue raised by Guillaume
see GEO-BON/bon-in-a-box-pipeline-engine#169 (comment)

.github/workflows/docker_runner-conda.yml

@@ -25,7 +25,7 @@ jobs:
         username: ${{ secrets.DOCKER_USERNAME }}
         password: ${{ secrets.DOCKER_PASSWORD }}
 
-    - name: Extract metadata (tags, labels) for Docker, main branch
+    - name: Extract metadata (tags, labels) for Docker
       if: github.ref == 'refs/heads/main'
       id: metadata-main
       uses: docker/metadata-action@v4
@@ -53,6 +53,6 @@ jobs:
         context: runners
         file: runners/conda-dockerfile
         push: true
-        tags: ${{ steps.meta.outputs.tags }}
-        labels: ${{ steps.meta.outputs.labels }}
+        tags: ${{ steps.metadata-main.outputs.tags || steps.metadata-staging.outputs.tags }}
+        labels: ${{ steps.metadata-main.outputs.labels || steps.metadata-staging.outputs.labels }}
 

.github/workflows/docker_runner-julia.yml

@@ -1,4 +1,4 @@
-name: Julia Runner, main branch
+name: Julia Runner
 
 on:
   workflow_dispatch:
@@ -50,6 +50,7 @@ jobs:
         context: runners
         file: runners/julia-dockerfile
         push: true
-        tags: ${{ steps.meta.outputs.tags }}
-        labels: ${{ steps.meta.outputs.labels }}
+        tags: ${{ steps.metadata-main.outputs.tags || steps.metadata-staging.outputs.tags }}
+        labels: ${{ steps.metadata-main.outputs.labels || steps.metadata-staging.outputs.labels }}
+
 

runners/conda-dockerfile

@@ -1,10 +1,6 @@
 FROM  condaforge/mambaforge
-
-ADD ./r-environment.yml /data/r-environment.yml
-
 WORKDIR /data
 
-
 # Setting Time zone (necessary to install cmake, + will persist at runtime)
 ENV TZ=Etc/UTC
 
@@ -29,6 +25,7 @@ RUN chmod 777 /.condarc
 # Permissions cannot be defined at mount time, hence we create empty folder with the appropriate permissions.
 RUN mkdir /.cache && mkdir /.cache/conda && chmod a+w /.cache/conda
 RUN mkdir /.conda && chmod a+w /.conda
+RUN mkdir /.config && chmod a+w /.config
 RUN mkdir /r-libs-user && chmod a+w /r-libs-user
 RUN mkdir /conda-env-yml && chmod a+w /conda-env-yml
 
@@ -39,13 +36,9 @@ RUN echo 'eval "$(conda shell.bash hook)"; source /opt/conda/etc/profile.d/mamba
 # See https://stackoverflow.com/a/74017557/3519951
 RUN sed -e '/[ -z "$PS1" ] && return/s/^/#/g' -i /root/.bashrc
 
+ADD ./r-environment.yml /data/r-environment.yml
 RUN mamba env create -f /data/r-environment.yml
 
-# Hide "error libmamba Could not open lockfile '/opt/conda/pkgs/cache/cache.lock'" when installing manually with non-root user
-# That error would not prevent the correct installation, but it looked like it to the user.
-RUN chmod -R 777 /opt/conda/pkgs/cache
-
-
 ## ADD CRAN PACKAGES HERE (for packages not found in anaconda.org)
 RUN bash --login -c "mamba activate rbase; R -e 'install.packages(c(\"CoordinateCleaner\", \
         \"geodata\", \
@@ -56,4 +49,11 @@ RUN bash --login -c "mamba activate rbase; R -e 'install.packages(c(\"Coordinate
 RUN bash --login -c "mamba activate rbase; R -e 'devtools::install_github(\"ReseauBiodiversiteQuebec/stac-catalogue\")'"
 RUN bash --login -c "mamba activate rbase; R -e 'devtools::install_github(\"connectscape/Makurhini\")'"
 
+ADD ./python-environment.yml /data/python-environment.yml
+RUN mamba env create -f /data/python-environment.yml
+
+# Hide "error libmamba Could not open lockfile '/opt/conda/pkgs/cache/cache.lock'" when installing manually with non-root user
+# That error would not prevent the correct installation, but it looked like it to the user.
+RUN chmod -R 777 /opt/conda/pkgs/cache
+
 RUN date +"%Y-%m-%d %R" > /version.txt

runners/python-environment.yml

@@ -0,0 +1,5 @@
+name: pythonbase
+channels:
+  - conda-forge
+dependencies:
+  - pystac