v 2.0.0

src/scicloj/.devcontainer/Dockerfile

@@ -1,5 +1,4 @@
 FROM clojure:${templateOption:imageTag}
-
 ARG USERNAME=vscode
 ARG USER_UID=1000
 ARG USER_GID=$USER_UID
@@ -23,3 +22,4 @@ USER $USERNAME
 SHELL ["/bin/bash", "-ec"]
 ENTRYPOINT ["bash"]
 
+\

src/scicloj/.devcontainer/devcontainer.json

@@ -4,45 +4,24 @@
 	},
 
 	"features": {
-		"ghcr.io/devcontainers/features/desktop-lite:1": {},
 		"ghcr.io/devcontainers-extra/features/apt-get-packages:1": {
-			"ppas": "ppa:ubuntuhandbook1/emacs",
-			"packages": "r-base-dev,emacs,rlwrap,fonts-hack"
-		},
-		"ghcr.io/devcontainers/features/python:1": {
-			"version": "latest"
+			"packages": "r-base-dev,rlwrap"
 		},
+		"ghcr.io/va-h/devcontainers-features/uv:1": {},
 		"ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {},
 		"ghcr.io/rocker-org/devcontainer-features/r-apt:0": {},
-		"ghcr.io/rocker-org/devcontainer-features/rstudio-server": {},
 		"ghcr.io/devcontainers/features/docker-in-docker:2": {},
-		"ghcr.io/devcontainers-extra/features/poetry:2": {},
 		"ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
 			"packages": "Rserve",
 			"additionalRepositories": "rforge= 'https://rforge.net'",
 			"installSystemRequirements": true
 		},
 		"ghcr.io/wxw-matt/devcontainer-features/command_runner:latest": {
-                        "command1": "bash < <(curl -s https://raw.githubusercontent.com/clojure-lsp/clojure-lsp/master/install)",
+         	            "command1": "bash < <(curl -s https://raw.githubusercontent.com/clojure-lsp/clojure-lsp/master/install)",
                         "command2": "bash < <(curl -s https://raw.githubusercontent.com/babashka/babashka/master/install)",
-			"command3": "bash -c 'wget https://raw.githubusercontent.com/technomancy/leiningen/stable/bin/lein -O /usr/local/bin/lein && chmod +x /usr/local/bin/lein'"
+			            "command3": "bash -c 'wget https://raw.githubusercontent.com/technomancy/leiningen/stable/bin/lein -O /usr/local/bin/lein && chmod +x /usr/local/bin/lein'"
                 }
 	},
-	"overrideFeatureInstallOrder": [
-	       "ghcr.io/rocker-org/devcontainer-features/r-apt",
-	       "ghcr.io/devcontainers-extra/features/apt-get-packages",
-	       "ghcr.io/rocker-org/devcontainer-features/r-packages"
-                ],	
-
-	"forwardPorts": [6080,12345],
-	"portsAttributes": {
-		"6080": {
-			"label": "desktop"
-		},
-		"12345": {
-			"label": "nrepl"
-		}
-	},
 	"customizations": {
 		"vscode": {
 			"extensions": [
@@ -51,9 +30,9 @@
 		}
 	},
 
-	"postAttachCommand":
-	{ "ide-setup": ["bash", "-c", "if [ -f \"/home/vscode/.setup-ide/setup-ide.sh\" ]; then /home/vscode/.setup-ide/setup-ide.sh; fi"],
-	  "prepare": ["bash","-c", "-i", "source ./.devcontainer/setup.sh"]
+	"onCreateCommand":
+	{ 
+	  "prepare": "./.devcontainer/setup.sh"
 
 
 	}

src/scicloj/.devcontainer/setup.sh

@@ -1,7 +1,3 @@
 #!/bin/bash -xe
 
 clj -Sthreads 1 -P
-mkdir -p .venv 
-poetry install
-tic -x .devcontainer/terminfo24bit.src
-echo "alias emacs='TERM=xterm-24bits emacs'" >> ~/.bashrc

src/scicloj/.gitignore

@@ -0,0 +1,11 @@
+.lsp
+.cpcache
+.clj-kondo
+.RData
+.Rhistory
+.calva
+.classes
+uv.lock
+classes
+.nrepl-port
+.venv

src/scicloj/NOTES.md

@@ -1,23 +1,24 @@
 # A template project featuring a devcontainer setup for Datascience with Clojure using several libraries from [scicloj](https://scicloj.github.io/)
 
-It sets up an dev container environment with several tool s and libaries for datascience in Clojure.
+It sets up an dev container environment with several tool s and libraries for datascience in Clojure.
 
 # Quickstart
 0. Install [devcontainer cli](https://github.com/devcontainers/cli)
 1. Run `devcontainer templates apply -t ghcr.io/scicloj/devcontainer-templates/scicloj` to create a devcontainer setup
    with default settings in your current directoty
 2. Open folder with VSCode / devcontainer / devpod / Codespaces and trigger/wait for container build
 3. "jack in" inside the devcontainer
-4. Enjoy Clojure and R  + python from Clojure  (using ClojisR + libpython-clj)
+4. run "uv sync" to syvc python environment with pyproject.toml
+5. Enjoy Clojure and R  + python from Clojure  (using ClojisR + libpython-clj)
 
 ## template options:
 image-tag: ubuntu LTS only and Java LTS 8,11,17,21 and if released on Dockerhub
 default image-tag: lastet ubuntu LTS + latest supported LTS JDK + latest released clojure (and available on Dockerhub)
 ## Customization
 
-5. Customize libraries
-    * deps.edn: add Clojure + Java libraries
-    * pyproject.toml: add python libraries into poetry config file
+5. Customize libraries in declarative way
+    * deps.edn:          add Clojure + Java libraries
+    * pyproject.toml:    add python libraries 
     * devcontainer.json: add R libraries (see [r-packages](ghcr.io/rocker-org/devcontainer-features/r-packages)
 
 
@@ -29,49 +30,34 @@ default image-tag: lastet ubuntu LTS + latest supported LTS JDK + latest release
 ## Installed inside devcontainer
 
 
-The purpose of this devcontainer setup is to support VSCode and (graphical) Emacs as IDEs.
+The purpose of this devcontainer setup is to support Clojure data science including Clojure integration with python and R
 
-### Supporting VSCode
-
-For supportring VSCode, nothing specific need to be done, as devcontainer support is build
-int VSCode. 
-
-### Supporting Emacs
-The Emacs support consists in setting up a noVNC desktop inclding Emacs in graphical mode.
-The VNC port is auto-forwarded and can be seen inside a browser window.
-It added as well a generic way to configure emacs, from `dotfiles`, see below.
 
 The provided devcontainer.json installs in the devcontainer:
 
 * Clojure (incl. clojisr and libpython-clj)
-* Python incl. poetry (packages can be added via changing the `pyproject.toml` in devcontainer.json)
+* 'uv' python package manager
 * R (packages can be added in devcontainer.json)
-   * incl. rstudio-server
-
+* pyproject.toml , which specifies python version and packages
 * deps.edn with Clojure libraries for Data science from scicloj
-* noVNC + lite desktop incl port forwarding
-* Emacs
 * quarto cli
 * docker-in-docker
 * leiningen
 * babashka
 * lsp
 
-### Graphical Emacs in web-noVNC
-In the default settings, we will get a vanilla Emacs running in noVNC.
-The Emacs setup can be configured via providing a specific script in a fixed location 
-, which can be most easly done using the dotfile support of devcontainer.
-
-See here: [dotfiles](https://code.visualstudio.com/docs/devcontainers/containers#_personalizing-with-dotfile-repositories)
-
-If there is a file in `/home/vscode/.setup-ide/setup-ide.sh` it will be executed after container creation.
-This can do "whatever" to configure Emacs from your own configuration.
-(Baically the script can do everything on the build container.)
-
-My `setup-ide.sh` configures Doom Emacs with my personal configuration.
 
 
 # Version history 
+## 2.0.0
+BREAKING CHANGE:
+- removed poetry
+- removed emacs
+- removed vnc
+- removed rstudio server
+- added uv
+- use Clojure 1.12.2.1565 images
+
 ## 1.1.3
 - fixed feature names from 'contrib' -> 'extra'
 

src/scicloj/deps.edn

@@ -1,7 +1,7 @@
 {:paths ["src" "resources"]
- :deps {org.clojure/clojure {:mvn/version "1.12.0"}
-        org.scicloj/noj {:mvn/version "2-beta5.1"}
-        }
+ :deps {org.clojure/clojure {:mvn/version "1.12.2"}
+        org.scicloj/noj {:mvn/version "2-beta18"}}
+
  :aliases
  {:build {:deps {io.github.clojure/tools.build {:mvn/version "0.10.3"}
                  slipset/deps-deploy {:mvn/version "0.2.2"}}

src/scicloj/devcontainer-template.json

@@ -1,6 +1,6 @@
 {
     "id": "scicloj",
-    "version": "1.1.3",
+    "version": "2.0.0",
     "name": "scicloj datascience devcontainer template",
     "description": "A devcontainer template supporting Clojure datascience with R and python interop",
     "documentationURL": "https://github.com/scicloj/devcontainer-templates/tree/main/src/scicloj",
@@ -11,14 +11,14 @@
             "description": "Tag of official Clojure image",
 
             "proposals": [
-                "temurin-8-tools-deps-1.12.0.1495-jammy",
-                "temurin-11-tools-deps-1.12.0.1495-jammy",
-                "temurin-17-tools-deps-1.12.0.1495-jammy",
-                "temurin-21-tools-deps-1.12.0.1495-jammy"
+                "temurin-8-tools-deps-1.12.2.1565-jammy",
+                "temurin-11-tools-deps-1.12.2.1565-jammy",
+                "temurin-17-tools-deps-1.12.2.1565-jammy",
+                "temurin-21-tools-deps-1.12.2.1565-jammy"
 
             ],
 
-            "default": "temurin-21-tools-deps-1.12.0.1495-jammy"
+            "default": "temurin-21-tools-deps-1.12.2.1565-jammy"
         }
 
     },

src/scicloj/pyproject.toml

@@ -1,7 +1,8 @@
-[tool.poetry]
-package-mode = false
+[project]
+name = "temp"
+version = "0.0"
+requires-python = "==3.13.7"
+dependencies = [
+"pandas"
+]
 
-
-[tool.poetry.dependencies]
-python = "^3.12"
-pandas = "2.2.3"

src/scicloj/pyproject.toml.deps

@@ -0,0 +1,8 @@
+[project]
+name = "temp"
+version = "0.0"
+requires-python = "==3.13.7"
+dependencies = [
+"pandas"
+]
+

src/scicloj/python.edn

@@ -1 +1,4 @@
-  {:python-executable   ".venv/bin/python"}
+{
+ :python-executable ".venv/bin/python" ; Linux
+ ;:python-executable ".venv/Scripts/python" ; Windows
+ }

src/scicloj/src/analyze.clj

@@ -0,0 +1,41 @@
+(ns scicloj.src.analyze
+  (:require [libpython-clj2.python :as py]
+            [libpython-clj2.require :as py-req]
+            [clojisr.v1.r :as r]
+            )
+  )
+(comment
+  ; getting started with python
+  (py/initialize!)
+
+  (py/run-simple-string "print (1+1)")
+
+
+  (def sys (py/import-module "sys"))
+
+  (println (py/py.- sys version))
+  (println (py/py.- sys path))
+
+
+  (py-req/require-python '[os])
+  (os/getcwd)
+
+  (py-req/require-python '[pandas :as pd]
+                         '[io :refer [StringIO]])
+  (def df (pd/read_csv (StringIO "a,b,c\n1,2,3\n4,5,6")))
+
+
+(comment
+  ; getting started with R
+  (r/r "1+1")
+  (r/r '(+ 1 2))
+
+
+  (r/require-r '[jsonlite])
+  (jsonlite/toJSON [1 2 3])
+  )
+
+
+
+(println "ok")
+(shutdown-agents)

test/scicloj/.gitignore

@@ -0,0 +1,5 @@
+uv.lock
+.cpcache
+classes
+.nrepl-port
+.venv

test/scicloj/pyproject.toml

@@ -0,0 +1,6 @@
+[project]
+name = "scicloj-test"
+version = "0.1.0"
+description = "Add your description here"
+requires-python = "==3.10.17"
+dependencies = ['pandas']

test/scicloj/python.edn

@@ -0,0 +1,4 @@
+{
+ :python-executable ".venv/bin/python" ; Linux
+ ;:python-executable ".venv/Scripts/python" ; Windows
+ }

test/scicloj/test.sh

@@ -3,18 +3,14 @@ cd $(dirname "$0")
 source test-utils.sh
 
 # Template specific tests
-check "distro" lsb_release -c
-#check "color" [ $(cat /tmp/color.txt | grep red) ]
-#check "libpython-clj" clj -e "(require '[libpython-clj2.python :refer [py. py.. py.-] :as py])(py/initialize!)(py/run-simple-string \"print(1+1)\")"
-#check "clojisr" clj -e "(require '[clojisr.v1.r :refer [r]])(r '(+ 1 2))"
-#check "pandas" clj -e "(require '[libpython-clj2.require :refer [require-python]])(require-python '[pandas :as pd])"
+check "distro" cat /etc/os-release
 check "clj" clj --version
-check "poetry" poetry --version
-check "bb" bb --version
+check "uv" uv --version
 check "R" R --version
-check "emacs" emacs --version
 check "lein" lein --version
-
-
+check "check" pwd && ls -la
+check "libpython-clj" uv sync --link-mode=copy && clj -Sdeps '{:deps {org.scicloj/noj {:mvn/version "2-beta18"}}}' -e '(require '\''[libpython-clj2.python :as py])(py/initialize!)(py/run-simple-string "print(1+1)")(shutdown-agents)' 
+check "clojisr" clj -Sdeps '{:deps {org.scicloj/noj {:mvn/version "2-beta18"}}}' -e '(require '\''[clojisr.v1.r :refer [r]])(r '\''(+ 1 2))(shutdown-agents)'
+check "pandas" uv sync && uv sync --link-mode=copy && clj  -Sdeps '{:deps {org.scicloj/noj {:mvn/version "2-beta18"}}}' -e '(require '\''[libpython-clj2.require :refer [require-python]])(require-python '\''[pandas :as pd])(shutdown-agents)'
 # Report result
 reportResults