docker: build image with nix instead of Dockerfile

Makefile

@@ -1,3 +1,23 @@
 .PHONY: data
+version=`cat VERSION`
+
 data:
 	Rscript ./initialise_data.R
+
+docker-image:
+	nix run .\#images.x86_64-linux.latest.copyToDockerDaemon
+
+release:
+	# Run tests and build + push the 2 docker images tagged `latest` and `X.X.X`
+	# according to the current version
+	nix run .\#unit_tests
+	nix run .\#test_ui
+	nix run .\#images.x86_64-linux.latest.copyTo -- docker://docker.io/juliendiot/plantbreedgame:latest
+	skopeo --insecure-policy copy docker://docker.io/juliendiot/plantbreedgame:latest docker://docker.io/juliendiot/plantbreedgame:$(version)
+
+dev-release:
+	# Run tests and build + push the a docker images tagged `development`
+	nix run .\#unit_tests
+	nix run .\#test_ui
+	nix run .\#images.x86_64-linux.latest.copyTo -- docker://docker.io/juliendiot/plantbreedgame:development
+

README.md

@@ -112,97 +112,50 @@ See the explanations below in the section "Usage".
 
 ## :whale2: Docker
 
-Thank to docker, you can deploy this application without not installing anything more than docker on your server.
+Thank to docker, you can deploy this application without installing anything more than docker on your server.
 
 To install docker please refer here: [ubuntu](https://docs.docker.com/install/linux/docker-ce/ubuntu/), [debian](https://docs.docker.com/install/linux/docker-ce/debian/), [other](https://docs.docker.com/install/).
 
 ### Deployment
 
 A docker image of this application is available on Docker Hub: [juliendiot/plantbreedgame](https://hub.docker.com/r/juliendiot/plantbreedgame).
 
+Those images are tagged in 3 different ways:
+- `latest`: The latest stable version
+- `development`: The latest development version
+- `X.X.X`: The image corresponding the plantBreedGame version `X.X.X`
+
+In the following commands, you can replace `juliendiot/plantbreedgame:latest` 
+with the version you want to use.
+
 #### 1st method
 
-The simplest way to deploy the application on a server using docker is with this command:
+For **testing purpose**, the simplest way to run the application using docker is with this command:
 
 ```sh
-docker run -d --rm --name plantbreedgame -p 80:3838 juliendiot/plantbreedgame
+docker run -d --rm --name plantbreedgame -p 80:3838 juliendiot/plantbreedgame:latest
 ```
 
 The application is then accessible on the host machine on port `80` at the path `/PlantBreedGame`, for example: `localhost:80/PlantBreedGame` on your personal computer.
 
-Be careful, stopping this container will erase all the progress of the players.
+Be careful ! **Stopping this container will erase all the progress of the players**.
 
 #### 2nd method
 
-This method is for people who want persistant game progress, a manual access to the `data` folder of the game and an access to the application's logs.
-
-In order to access to the `data` folder of the game, we must first extract this folder from the image:
-
-```sh
-docker run -d --rm --name plantbreedgame juliendiot/plantbreedgame
-docker cp plantbreedgame:/srv/shiny-server/PlantBreedGame/data /host/path/to/appData
-docker stop plantbreedgame
-chgrp docker -R /host/path/to/appData/data
-chmod 774 /host/path/to/appData/data
-chmod 664 /host/path/to/appData/data/breeding-game.sqlite
-```
-
-Then we must create a folder for the logs:
-
-```sh
-mkdir /host/path/to/log
-chgrp docker /host/path/to/log
-```
+For actual game session, you need to specify to docker a persistent
+["volume"](https://docs.docker.com/engine/storage/volumes/#start-a-container-with-a-volume)
+where it can save and keep the game data when the container is stoped.
 
-We can now mount these folders on a new running the container :
+With the command below:
 
 ```sh
 docker run -d --rm --name plantbreedgame -p 80:3838 \
-    -v /host/path/to/appData:/srv/shiny-server/PlantBreedGame/data \
-    -v /host/path/to/log:/var/log/shiny-server/ \
-    juliendiot/plantbreedgame
-```
-
-Finally, we must give the same group id to the container's "shiny" group than the host's "docker" group:
-
-```sh
-docker exec -u 0 -it plantbreedgame groupmod -g $(cut -d: -f3 < <(getent group docker)) shiny
-```
-
-#### debug
-
-To access to the a bash console from inside the container use:
-
-```sh
-docker exec -u 0 -it plantbreedgame bash
-```
-
-### custom build
-
-If you want to use specific game parameters (define in the file `plantbreedgame_setup.Rmd`) you can build your own docker image:
-
-1. get the application code:
-
-```sh
-wget https://github.com/timflutre/PlantBreedGame/archive/master.zip
-unzip master.zip
-mv PlantBreedGame-master PlantBreedGame
-```
-
-or
-
-```sh
-git clone --depth=1 https://github.com/timflutre/PlantBreedGame.git
-```
-
-2. move in the app code folder and build a new image:
-
-```sh
-cd PlantBreedGame
-docker build -t customplantbreedgame ./
+    -v /host/path/to/plantBreedGameData:/var/lib/plantBreedGame \
+    juliendiot/plantbreedgame:latest
 ```
 
-You can then run this image by using the same commands as above replacing `juliendiot/plantbreedgame` by `customplantbreedgame`
+The game data will be saved in the host machine at `/host/path/to/plantBreedGameData`.
+You can select any location you want.
 
 
 # Usage
@@ -211,17 +164,16 @@ You can then run this image by using the same commands as above replacing `julie
 
 To start playing, the game need some specific data (eg. the genotypes and haplotypes of the initial population, a data-base...). This initialisation can be done through the game.
 
-The first time you run the application, most of the game menus will show a message asking you to initialise the game. To do so you need to go to the `Admin` menue, and in `Game Initialisation` tab. There you will find a button that will start the game initialisation. Once the initialisation is completed (which takes about 2 minutes), the page will automatically reload and you will be able to connect and play the game.
+The first time you run the application, most of the game menus will show a message asking you to initialise the game. To do so you need to go to the `Admin` menu, and in `Game Initialisation` tab. There you will find some parametres you can tweak to customise the game and a button that will start the game initialisation. Once the initialisation is completed (which takes about 2 minutes), the page will automatically reload and you will be able to connect and play the game.
 
 The game initialisation will automatically create an `admin` breeder with the default password `1234`.
 
 If the game have already been initialise, it is also possible to re-initialise it to start a new "fresh game". However in such case **all the data of the game will be lost**.
 
-> NOTE: Currently the game do not let you choose the game initialisation parameters, in order to change them, you need to manually modify the file `plantbreedgame_setup.Rmd` befor proceding to the initialisation. In a near future, you will be able to set the intialisation parameters from the game.
 
 ## How to play
 
-Once the application is installed and working, _please_ read the game rules (tab `How to play?`) and start by downloading the initial data set as well as example files showing how requests should be formatted (all files listed at the bottom of the tab `How to play?`).
+Once the application is installed and working, please read the game rules (tab `How to play?`) and start by downloading the initial data set as well as example files showing how requests should be formatted (all files listed at the bottom of the tab `How to play?`).
 
 Before making any request, such as phenotyping, you need to log in (tab `Identification`).
 To get a sense of how the interface works, you can use the "test" breeder with the "tester" status which doesn't require any password and isn't subject to time restriction.

flake.nix

@@ -3,16 +3,25 @@
   inputs = {
     nixpkgs.url = "nixpkgs/nixos-24.05";
     flake-utils.url = "github:numtide/flake-utils";
+
+    nix2container.url = "github:nlewo/nix2container";
+    nix2container.inputs.nixpkgs.follows = "nixpkgs";
   };
 
   outputs = {
     self,
     nixpkgs,
     flake-utils,
+    nix2container,
   }:
     flake-utils.lib.eachDefaultSystem (
       system: let
         pkgs = import nixpkgs {inherit system;};
+        nix2containerPkgs = nix2container.packages.${system};
+        imageBuilder =
+          (import ./nix_package/image.nix {inherit nix2containerPkgs pkgs;})
+          .builder;
+
         Rpkgs = pkgs;
         R-packages = with Rpkgs.rPackages; [
           shiny
@@ -79,6 +88,7 @@
             pkgs.zip
             pkgs.nodejs_20
             (pkgs.playwright-driver.override {nodejs = pkgs.nodejs_20;})
+            pkgs.skopeo
           ];
         };
 
@@ -139,6 +149,15 @@
           src = pkgs.lib.sources.cleanSource ./.;
         };
         packages.default = packages.plantBreedGame;
+
+        images = {
+          latest = let
+          in (imageBuilder {
+            imageName = "plantBreedGame";
+            plantBreedGame = packages.plantBreedGame;
+            tag = "latest";
+          });
+        };
       }
     );
 }

nix_package/image.nix

@@ -0,0 +1,62 @@
+{
+  nix2containerPkgs,
+  pkgs,
+}: {
+  builder = {
+    imageName ? null,
+    plantBreedGame ? null,
+    tag ? "latest",
+  }: let
+    setTimezone = pkgs.runCommand "setTimezone" {} ''
+      mkdir -p $out/etc
+      ln -s ${pkgs.tzdata}/share/zoneinfo/Asia/Tokyo $out/etc/localtime
+    '';
+  in
+    nix2containerPkgs.nix2container.buildImage {
+      name = imageName;
+      tag = tag;
+      maxLayers = 100;
+
+      # force plantBreedGame and its dependencies to be in different layers
+      layers = [
+        # dependencies layer
+        (nix2containerPkgs.nix2container.buildLayer {
+          deps = plantBreedGame.buildInput;
+          maxLayers = 90;
+        })
+        # plantBreedGame layer
+        (nix2containerPkgs.nix2container.buildLayer {
+          deps = plantBreedGame.buildInput;
+        })
+      ];
+
+      copyToRoot = [
+        (pkgs.buildEnv {
+          name = "root";
+          paths = with pkgs;
+          with pkgs.dockerTools; [
+            plantBreedGame
+            setTimezone
+
+            fakeNss
+            tzdata
+
+            bashInteractive
+            coreutils
+            usrBinEnv
+            binSh
+          ];
+          ignoreCollisions = false;
+          pathsToLink = ["/bin" "/var" "/run" "/tmp" "/etc" "/share"];
+        })
+      ];
+
+      config = {
+        WorkingDir = "/";
+        Run = ["touch" "/toto.txt"];
+        Volume = "/var/lib/plantBreedGame";
+        Cmd = ["${plantBreedGame}/bin/plantBreedGame" "--host" "0.0.0.0" "--port" "3838"];
+        Expose = 3838;
+      };
+    };
+}