Update flake and potery deps

[anpin]

This PR:

• updates flake and poetry dependencies
• fixes broken evaluation for ocaml
• updates deprecated bits such as cargo fetchers and poetry dev-deps groups
• updates documentation for custom kernel as it was misleading

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[anpin]

fixing ocaml kernel requires knowledge of some deep magic beyond my current understanding

[I 2025-02-13 21:47:20.765 ServerApp] Kernel started: 24b40db1-ce0c-4f76-ba46-5b3bf34dc4bb
/nix/store/p2s5ccpqgzgcq16b277rmfqg5bv0aflx-extra-ocaml-path: line 2: declare: BASHOPTS: readonly variable
[I 2025-02-13 21:47:23.754 ServerApp] AsyncIOLoopKernelRestarter: restarting kernel (1/5), new random ports
/nix/store/p2s5ccpqgzgcq16b277rmfqg5bv0aflx-extra-ocaml-path: line 2: declare: BASHOPTS: readonly variable
[I 2025-02-13 21:47:26.769 ServerApp] AsyncIOLoopKernelRestarter: restarting kernel (2/5), new random ports
/nix/store/p2s5ccpqgzgcq16b277rmfqg5bv0aflx-extra-ocaml-path: line 2: declare: BASHOPTS: readonly variable
[I 2025-02-13 21:47:29.782 ServerApp] AsyncIOLoopKernelRestarter: restarting kernel (3/5), new random ports
/nix/store/p2s5ccpqgzgcq16b277rmfqg5bv0aflx-extra-ocaml-path: line 2: declare: BASHOPTS: readonly variable
[I 2025-02-13 21:47:32.795 ServerApp] AsyncIOLoopKernelRestarter: restarting kernel (4/5), new random ports
/nix/store/p2s5ccpqgzgcq16b277rmfqg5bv0aflx-extra-ocaml-path: line 2: declare: BASHOPTS: readonly variable
[I 2025-02-13 21:47:35.808 ServerApp] AsyncIOLoopKernelRestarter: restarting kernel (5/5), new random ports
/nix/store/p2s5ccpqgzgcq16b277rmfqg5bv0aflx-extra-ocaml-path: line 2: declare: BASHOPTS: readonly variable
[W 2025-02-13 21:47:38.823 ServerApp] AsyncIOLoopKernelRestarter: restart failed

[anpin]

hey @balsoft, pinging you since you are opam-nix maintainer. maybe you can help with this one?

[anpin]

I tried this very crude fix and it got me further

diff --git a/modules/kernels/ocaml/default.nix b/modules/kernels/ocaml/default.nix
index a023be6..ed17a50 100644
--- a/modules/kernels/ocaml/default.nix
+++ b/modules/kernels/ocaml/default.nix
@@ -76,6 +76,15 @@
         name = "extra-ocaml-path";
         packages = ocamlPackageDerivations ++ allRuntimePackages;
       };
+      patchedRuntimeEnv = pkgs.runCommand "patched-extra-ocaml-path" {
+        inherit runtimeEnv;
+      } ''
+        sed -e '/^declare -r BASH/d'\
+            -e '/^declare -ar BASH/d'\
+            -e '/^declare -ir/d'\
+            -e '/^declare -r/d'\
+            ${runtimeEnv.inputDerivation} > $out
+      '';
       ocamlinit = ''
         #use "${scope.ocamlfind}/lib/ocaml/${scope.ocaml.version}/site-lib/topfind";;
         Topfind.log:=ignore;;
@@ -93,7 +102,7 @@
             #     This is not the case with the nix store, so we have to point it to
             #     the corresponding store paths manually.
             wrapProgram $out/bin/$filename \
-              --run 'source ${runtimeEnv.inputDerivation}; source $stdenv/setup' \
+              --run 'source ${patchedRuntimeEnv}; source $stdenv/setup' \
               --suffix CAML_LD_LIBRARY_PATH : "$CAML_LD_LIBRARY_PATH"
           done
         '';
(END)

[I 2025-02-13 22:28:29.516 ServerApp] Kernel started: 4b8410a2-46c7-4989-a372-e42ee0a2b9b6
install: cannot create regular file '/build/env-vars': No such file or directory
2025-02-14T01:28:29  STDOUT>> Findlib has been successfully loaded. Additional directives:
2025-02-14T01:28:29  STDOUT>>   #require "package";;      to load a package
2025-02-14T01:28:29  STDOUT>>   #list;;                   to list the available packages
2025-02-14T01:28:29  STDOUT>>   #camlp4o;;                to load camlp4 (standard syntax)
2025-02-14T01:28:29  STDOUT>>   #camlp4r;;                to load camlp4 (revised syntax)
2025-02-14T01:28:29  STDOUT>>   #predicates "p,q,...";;   to set these predicates
2025-02-14T01:28:29  STDOUT>>   Topfind.reset();;         to force that packages will be reloaded
2025-02-14T01:28:29  STDOUT>>   #thread;;                 to enable threads
2025-02-14T01:28:29  STDOUT>>