Update container files

* activate parpe python environment by default
* fix git_archival.txt / setuptools_scm
* avoid unnecessary full rebuilds when modifying Dockerfile

.git_archival.txt

@@ -0,0 +1 @@
+python/.git_archival.txt

.gitattributes

@@ -1,3 +1,2 @@
-.git_archival.txt  export-subst
 python/.git_archival.txt  export-subst
 

.github/workflows/deploy_dockerhub.yml

@@ -24,13 +24,13 @@ jobs:
     if: needs.check-secret.outputs.secrets-defined == 'true'
     steps:
     - uses: actions/checkout@master
-    - run: git archive -v -o container/charliecloud/parpe_base/parpe.tar.gz --format=tar.gz HEAD
+    - run: git archive -v -o container/charliecloud/container_files/parpe.tar.gz --format=tar.gz HEAD
     - name: Publish to Registry
       uses: elgohr/Publish-Docker-Github-Action@v5
       with:
         name: dweindl/parpe
         username: ${{ secrets.DOCKER_USERNAME }}
         password: ${{ secrets.DOCKER_PASSWORD }}
-        workdir: container/charliecloud/parpe_base/
+        workdir: container/charliecloud/
         dockerfile: Dockerfile
         tag_names: true

container/charliecloud/parpe_base/Dockerfile → container/charliecloud/Dockerfile

@@ -1,6 +1,6 @@
 FROM ubuntu:24.04
 
-COPY . /container-files
+COPY /container_files /container-files
 
 RUN /container-files/install.sh && rm -rf /tmp && mkdir /tmp
 
@@ -9,7 +9,7 @@ ENV CC clang
 ENV CXX clang++
 ENV OMPI_CC clang
 ENV OMPI_CXX clang++
-RUN /container-files/install_parpe.sh
+RUN /container-files/install_parpe.sh && echo "source /parPE/build/venv/bin/activate" >> /etc/bash.bashrc
 
 ENV PARPE_DIR "/parPE"
 

doc/parpe_with_charliecloud.md

@@ -22,8 +22,8 @@ This will create the parPE base image *from parPE from github*
 takes about 10'):
 
 ```shell
-git archive -v -o container/charliecloud/parpe_base/parpe.tar.gz --format=tar.gz HEAD
-cd container/charliecloud/parpe_base
+git archive -v -o container/charliecloud/container_files/parpe.tar.gz --format=tar.gz HEAD
+cd container/charliecloud/
 ch-build -t parpe .
 ```
 

misc/venv.sh

@@ -38,6 +38,6 @@ if [[ ! -d "${venv_dir}" ]]; then
 
     # install parPE
     cd "${parpe_root}/python"
-    pip3 install -e .
+    pip3 install -vvve .
     #pip3 install https://github.com/ICB-DCM/PEtab/archive/develop.zip
 fi