Merge branch 'update-numbering' into 'docs'

update dockerfile doc to follow the examples

See merge request !31

.gitlab-ci.yml

@@ -28,11 +28,13 @@ fetch_fragments:
     - image_list.rst
 
 
-pages:
+
+# as not named pages, the gitlab pages will not be updated
+check_pages_build:
   stage: build
   needs: ["fetch_fragments"]
   rules:
-    - if: $CI_COMMIT_BRANCH == "docs"
+    - if: $CI_COMMIT_BRANCH != "docs"
   image: python:3.10
   script:
     - mv image_list.rst source/user_guide/
@@ -43,4 +45,11 @@ pages:
     - mv build/html/ ./public
   artifacts:
     paths:
-      - public
\ No newline at end of file
+      - public
+
+
+
+pages:
+  extends: check_pages_build
+  rules:
+    - if: $CI_COMMIT_BRANCH == "docs"
\ No newline at end of file

source/user_guide/configure_image.rst

@@ -14,16 +14,18 @@ Here, you can see the content of the ``Dockerfile``:
 
 
         # Build image from the base image, previously configured for you
-        FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.9-slim-bullseye
+        # Full list of images can be found at 
+        # https://hub.pages.pasteur.fr/shiny-k8s/user_guide/configure_image.html#image-list
+        FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.9-slim-bullseye--1.5.22.1017
 
         # Add workdir information
         WORKDIR /srv/shiny-server/
 
-        # install additional dependencies, comment the block if you don't have one
-        RUN apt-get update \
-        && apt-get install -y \
-                wget \
-        && rm -rf /var/lib/apt/lists/*
+        # Install additional dependencies, uncomment the block if you have one, and edit/duplicate line 12
+        # RUN apt-get update \
+        #  && apt-get install -y \
+        #         your-system-dependency \
+        #  && rm -rf /var/lib/apt/lists/*
 
         # Copy your dependencies, destination filename must be "packages_to_install.csv"
         COPY ./requirements.txt /opt/scripts/requirements.txt
@@ -48,16 +50,18 @@ Here, you can see the content of the ``Dockerfile``:
 
 
         # Build image from the base image, previously configured for you
-        FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.3.1
+        # Full list of images can be found at 
+        # https://hub.pages.pasteur.fr/shiny-k8s/user_guide/configure_image.html#image-list
+        FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.3.1--1.5.22.1017
 
         # Add workdir information
         WORKDIR /srv/shiny-server/
 
-        # install additional dependencies, comment the block if you don't have one
-        RUN apt-get update \
-        && apt-get install -y \
-                wget \
-        && rm -rf /var/lib/apt/lists/*
+        # Install additional dependencies, uncomment the block if you have one, and edit/duplicate line 12
+        # RUN apt-get update \
+        #  && apt-get install -y \
+        #         your-system-dependency \
+        #  && rm -rf /var/lib/apt/lists/*
 
         # Copy your dependencies, destination filename must be "packages_to_install.csv"
         COPY ./my_packages_to_install.csv /opt/scripts/packages_to_install.csv
@@ -89,7 +93,9 @@ Line 1: The base image, with the right version
 
 
         # Build image from the base image, previously configured for you
-        FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.9-slim-bullseye
+        # Full list of images can be found at 
+        # https://hub.pages.pasteur.fr/shiny-k8s/user_guide/configure_image.html#image-list
+        FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.9-slim-bullseye--1.5.22.1017
 
     .. code-tab:: Dockerfile
         :caption: R
@@ -97,7 +103,9 @@ Line 1: The base image, with the right version
 
 
         # Build image from the base image, previously configured for you
-        FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.3.1
+        # Full list of images can be found at 
+        # https://hub.pages.pasteur.fr/shiny-k8s/user_guide/configure_image.html#image-list
+        FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.3.1--1.5.22.1017
 
 
 The ``FROM ...`` indicate which base image should be used, the image contains:
@@ -130,7 +138,7 @@ Line 5: Working Directory
         :caption: Python & R
         :linenos:
         :selected:
-        :lineno-start: 4
+        :lineno-start: 6
 
         # Add workdir information
         WORKDIR /srv/shiny-server/
@@ -138,7 +146,7 @@ Line 5: Working Directory
 We set the **current working directory** to ``/srv/shiny-server/`` .
 
 
-Lines 8-11: The system dependencies
+Lines 10-13: The system dependencies
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. tabs::
@@ -147,26 +155,30 @@ Lines 8-11: The system dependencies
         :caption: Python & R
         :linenos:
         :selected:
-        :lineno-start: 7
+        :lineno-start: 9
 
-        # install additional dependencies, comment the block if you don't have one
-        RUN apt-get update \
-        && apt-get install -y \
-                wget \
-        && rm -rf /var/lib/apt/lists/*
+        # Install additional dependencies, uncomment the block if you have one, and edit/duplicate line 12
+        # RUN apt-get update \
+        #  && apt-get install -y \
+        #         your-system-dependency \
+        #  && rm -rf /var/lib/apt/lists/*
 
 
 Some of your package dependencies require system dependencies  (such as 
 `graphviz-dev <https://packages.ubuntu.com/graphviz-dev>`_ for
 `pygraphviz <https://pypi.org/project/pygraphviz/>`_).
 
-To add such dependencies, duplicate line 10, and replace **wget** with your
-dependencies.
+To add such dependencies, 
+uncomment the bloc 10-13, 
+adapte/duplicate line 12, 
+and replace **your-system-dependency** with your actual dependency.
+We recommend you to specify one dependency per line, its helps later investigation
+when searching for why a dependency have been added.
 
-If you have **no additional system dependencies** you can remove this block.
+If you have **no additional system dependencies** you can keep this block commented.
 
 
-Lines 14-17: The package dependencies
+Lines 16-19: The package dependencies
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. tabs::
@@ -174,7 +186,7 @@ Lines 14-17: The package dependencies
     .. code-tab:: Dockerfile
         :caption: Python
         :linenos:
-        :lineno-start: 13
+        :lineno-start: 15
         :selected:
 
         # Copy your dependencies, destination filename must be "packages_to_install.csv"
@@ -187,7 +199,7 @@ Lines 14-17: The package dependencies
     .. code-tab:: Dockerfile
         :caption: R
         :linenos:
-        :lineno-start: 13
+        :lineno-start: 15
 
         # Copy your dependencies, destination filename must be "packages_to_install.csv"
         COPY ./my_packages_to_install.csv /opt/scripts/packages_to_install.csv
@@ -196,8 +208,8 @@ Lines 14-17: The package dependencies
         RUN Rscript /opt/scripts/install_r_packages.R
 
 
-The package dependencies are copied into the images line 14, 
-and installed line 17. The format of the file listing the dependencies depends
+The package dependencies are copied into the images line 16, 
+and installed line 19. The format of the file listing the dependencies depends
 on the language you use:
 
 
@@ -244,7 +256,7 @@ If can be from cran, from bioconductor, or even a github package.
     tidyverse/tibble; github package
 
 
-Line 20: Grant shiny to create bookmark state
+Line 22: Grant shiny to create bookmark state
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. tabs::
@@ -253,7 +265,7 @@ Line 20: Grant shiny to create bookmark state
         :caption: Python & R
         :linenos:
         :selected:
-        :lineno-start: 19
+        :lineno-start: 21
 
         # grant shiny to created bookmark state directory in this directory
         RUN chown shiny:shiny /var/lib/shiny-server
@@ -261,7 +273,7 @@ Line 20: Grant shiny to create bookmark state
 In order to run your application, the user ``shiny`` must be allow to write file in 
 ``/var/lib/shiny-server`` directory .
 
-Line 23: Copy your app into the image
+Line 25: Copy your app into the image
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. tabs::
@@ -270,7 +282,7 @@ Line 23: Copy your app into the image
         :caption: Python & R
         :linenos:
         :selected:
-        :lineno-start: 22
+        :lineno-start: 24
 
         # Copy you shiny app
         COPY ./my_project /srv/shiny-server
@@ -280,7 +292,7 @@ Line 23: Copy your app into the image
 At that moment you copy you app in the image.
 Keep in mind that this folder name :ref:`can be adapted <Custom source dir name>`.
 
-Line 26: Grant shiny to write output data
+Line 28: Grant shiny to write output data
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. tabs::
@@ -289,7 +301,7 @@ Line 26: Grant shiny to write output data
         :caption: Python & R
         :linenos:
         :selected:
-        :lineno-start: 25
+        :lineno-start: 27
 
         # grant shiny to use www folder
         RUN chown shiny:shiny /srv/shiny-server/www