uv integration

.devcontainer/Dockerfile

@@ -0,0 +1,25 @@
+FROM clojure:temurin-21-tools-deps-1.11.3.1456-jammy
+
+ARG USERNAME=vscode
+ARG USER_UID=1000
+ARG USER_GID=$USER_UID
+
+# Create the user
+RUN groupadd --gid $USER_GID $USERNAME \
+    && useradd --uid $USER_UID --gid $USER_GID -m $USERNAME \
+    #
+    # [Optional] Add sudo support. Omit if you don't need to install software after connecting.
+    && apt-get update \
+    && apt-get install -y sudo \
+    && echo $USERNAME ALL=\(root\) NOPASSWD:ALL > /etc/sudoers.d/$USERNAME \
+    && chmod 0440 /etc/sudoers.d/$USERNAME
+
+# ********************************************************
+# * Anything else you want to do like clean up goes here *
+# ********************************************************
+
+# [Optional] Set the default user. Omit if you want to keep the default as root.
+USER $USERNAME
+SHELL ["/bin/bash", "-ec"]
+ENTRYPOINT ["bash"]
+

.devcontainer/devcontainer.json

@@ -0,0 +1,38 @@
+{
+	"build": {
+		"dockerfile": "Dockerfile"
+	},
+
+	"features": {
+		"ghcr.io/devcontainers/features/desktop-lite:1": {},
+		"ghcr.io/devcontainers-contrib/features/apt-get-packages:1": {
+			"packages": "r-base-dev,rlwrap,expect"
+		},
+		"ghcr.io/devcontainers/features/python: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/r-packages:1": {},
+		"ghcr.io/wxw-matt/devcontainer-features/command_runner:latest": {
+                        "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'"
+				},
+				"ghcr.io/wxw-matt/devcontainer-features/command_runner:0": {},
+				"ghcr.io/va-h/devcontainers-features/uv:1": {}
+	},
+	"overrideFeatureInstallOrder": [
+	       "ghcr.io/rocker-org/devcontainer-features/r-apt",
+	       "ghcr.io/devcontainers-contrib/features/apt-get-packages",
+	       "ghcr.io/rocker-org/devcontainer-features/r-packages"
+                ],	
+
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"betterthantomorrow.calva"
+			]
+		}
+	}
+
+
+}

.gitignore

@@ -20,4 +20,8 @@ a.out
 *.iml
 .lsp
 .clj-kondo
-pregen-ffi-test
+pregen-ffi-test
+.calva
+.lock
+pyproject.toml
+uv.lock

deps.edn

@@ -3,11 +3,15 @@
         cnuernber/dtype-next    {:mvn/version "10.124"}
         net.java.dev.jna/jna    {:mvn/version "5.12.1"}
         org.clojure/data.json   {:mvn/version "1.0.0"}
+        cheshire/cheshire {:mvn/version "5.13.0"}
+        scicloj/clojisr {:mvn/version "1.0.0"}
         ;;Replace me with caffeine...
         com.google.guava/guava  {:mvn/version "31.1-jre"}}
+
+
 
  :aliases {:dev
-           {:extra-deps {criterium/criterium {:mvn/version"0.4.5"}
+           {:extra-deps {criterium/criterium {:mvn/version "0.4.5"}
                          ch.qos.logback/logback-classic {:mvn/version "1.1.3"}}}
            :fastcall
            {:jvm-opts ["-Dlibpython_clj.manual_gil=true"]}
@@ -71,4 +75,6 @@
             :exec-args {:installer :local
                         :artifact "target/libpython-clj.jar"}}
 
-           }}
+           }
+
+ }

python.edn.example

@@ -0,0 +1,8 @@
+{
+ ;:python-version "3.10.16"
+ ;:python-deps ["openai==1.58.1"
+ ;              "langextract"]
+ :python-executable ".venv/Scripts/python"
+ ;:pre-initialize-fn libpython-clj2.python.uv/sync-python-setup!
+
+}

src/libpython_clj2/python.clj

@@ -113,6 +113,7 @@ user> (py/py. np linspace 2 3 :num 10)
     (let [python-edn-opts (-> (try (slurp "python.edn")
                                    (catch java.io.FileNotFoundException _ "{}"))
                               clojure.edn/read-string)
+          _ (log/debugf "Pre-initialize-fn %s" (some-> python-edn-opts :pre-initialize-fn))
           _ (some-> python-edn-opts :pre-initialize-fn requiring-resolve (apply []))
           options (merge python-edn-opts options)
           info (py-info/detect-startup-info options)
@@ -819,3 +820,5 @@ user> c
   [symbols input]
   `(let [~symbols ~input]
      ~@(for [s symbols] `(def ~s ~s))))
+
+

src/libpython_clj2/python/uv.clj

@@ -0,0 +1,72 @@
+(ns libpython-clj2.python.uv
+  (:require
+   [clojure.edn :as edn]
+   [clojure.java.process :as process]
+   [clojure.string :as str]
+   [cheshire.core :as json]
+   [clojure.java.process :as proc]))
+
+(defn- write-pyproject-toml! [deps-edn]
+
+  (let [python-deps
+        (:python-deps deps-edn)
+
+        python-version (:python-version deps-edn)
+
+        py-project-header-lines ["[project]"
+                                 "name = \"temp\""
+                                 "version = \"0.0\""
+                                 (format "requires-python = \"==%s\"" python-version) 
+                                 ]
+        python-deps-lines
+        (map
+         (fn [dep]
+           (format "\"%s\"," dep))
+         python-deps)
+
+        py-project-lines
+        (concat
+         py-project-header-lines
+         ["dependencies = ["]
+         python-deps-lines
+         "]\n")]
+
+    (spit "pyproject.toml"
+          (str/join "\n" py-project-lines))))
+
+(defn- char-seq
+  [^java.io.Reader rdr]
+  (let [chr (.read rdr)]
+    (when (>= chr 0)
+      (do
+        ;(def chr chr)
+        (print (char (Integer. chr)))
+        (flush)
+        (cons chr (lazy-seq (char-seq rdr)))))))
+
+
+(defn- start-and-print! [process-args]
+  (let [p(apply process/start process-args)]
+
+    (with-open [in-rdr (java.io.InputStreamReader. (.getInputStream p))
+                err-rdr (java.io.InputStreamReader. (.getErrorStream p))]
+
+
+
+      (dorun (char-seq in-rdr))
+      (dorun (char-seq err-rdr)))))
+
+
+(defn sync-python-setup! 
+  "Synchronize python venv at .venv with 'uv sync'."
+  []
+  (println "Synchronize python venv at .venv with 'uv sync'. This might take a few minutes")
+  (let [deps-edn
+        (->
+         (slurp "python.edn")
+         edn/read-string)]
+    (write-pyproject-toml! deps-edn)
+    (start-and-print! ["uv" "sync" "--managed-python" "--python" (-> deps-edn :python-version)])))
+
+
+

topics/environments.md

@@ -14,3 +14,59 @@ Conda requires that we set the LD_LIBRARY_PATH to the conda install.
 
 * [example conda repl launcher](https://github.com/clj-python/libpython-clj/blob/master/scripts/conda-repl)
 * [libpython-clj issue for Conda](https://github.com/clj-python/libpython-clj/issues/18)
+
+
+
+## uv
+
+When you are using the (awesome !) python package manager [uv](https://docs.astral.sh/uv/) we provide a nice integration, which allows to auto-mange 
+declarative python environments.
+
+Assuming that you have 'uv' installed (it exists for Linux, Windows , Mac) you can specify and auto-setup a local python venv incl. python version by adding the following to `python.edn`
+(Linux example)
+
+```
+:python-version "3.10.16"
+:python-deps ["openai==1.58.1"
+              "langextract"]
+:python-executable ".venv/bin/python"
+:pre-initialize-fn libpython-clj2.python.uv/sync-python-setup!
+```
+
+The versions specification takes the same values as in uv, so would allow ranges a swell, for examples. We suggest to use precise versions, if possible
+
+Having this, on  a call to `(py/initialize!)` a python venv will be created/updated to match the python version and the specified packages. This calls behind the scenes `uv sync` so the spec and the venv are "brought in sync". 
+
+Re-syncing can be as well called manually (while the Clojure repl runs), invoking directly `(libpython-clj2.python.uv/sync-python-setup!)`
+
+### ux on Windows
+
+On Windows we need to use:
+`:python-executable ".venv/Scripts/python"`
+
+as the python executable.
+
+### Performance and progress logging
+
+uv is very fast, usualy package installations and even python installations run in under one minute.
+
+It was not possible to print progress logging output from the 'uv sync' run, so please be patient if nothings happens for a while, after changing python version or adding (larger) python packages.
+
+If you don't want to wait, you can just "kill the clojure process" and run `uv sync` by hand (which prints the logging).
+The integration creates an updated "pyproject.toml" file on disk, which `uv sync` will process.
+
+### Caveat
+
+We have noticed that under Windows for some python versions  `libpython-clj` does not setup the python library path correctly, resulting in python libraries not found using for example: `(py/import-module "xxx")`
+
+This is visible by inspecting python `sys.path`, which should contain `.venv/` via `(py/run-simple-string "import sys; print(sys.path)")`,
+
+`sys.path` should contain something like
+`c:\\Users\\behrica\\Repos\\tryLangExtract\\.venv`
+
+This can be fixed as by running after `(py/initialize!)` the following:
+
+Windows: `(py/run-simple-string "import sys; sys.path.append('.venv/Lib/site-packages')")`
+Linux: `(py/run-simple-string "import sys; sys.path.append('/.venv/lib/<python_version>/site-packages')")`
+
+Not sure, if the precise paths can change across python versions. They can be discovered by looking into `.venv` directory and see where precisely the "site-packages" directory is located.