Switch to hdf5-metno (#300)

## Summary of changes

- Switches to `hdf5-metno` from `hdf5` which is now unmaintained (see
aldanor/hdf5-rust#295)
- Install libhdf5 via build and static link rather than via Nix

## Instruction for review/testing

- Code review
- See that `nexus-writer` still writes valid NeXus files

Cargo.toml

@@ -28,7 +28,7 @@ clap = { version = "4.5", features = ["derive", "env"] }
 crossterm = "0.26.1"
 flatbuffers = "22.12.6"
 glob = "0.3.2"
-hdf5 = "0.8.1"
+hdf5 = { package = "hdf5-metno", version = "0.9.4", features = ["static"] }
 itertools = "0.13.0"
 lazy_static = "1.5.0"
 metrics = "0.22.3"

flake.nix

@@ -21,9 +21,6 @@
       system: let
         pkgs = (import nixpkgs) {
           inherit system;
-          overlays = [
-            (import ./nix/overlays/hdf5.nix)
-          ];
         };
 
         toolchain = fenix.packages.${system}.toolchainOf {
@@ -41,23 +38,16 @@
         version = workspaceCargo.workspace.package.version;
         gitRevision = self.shortRev or self.dirtyShortRev;
 
-        hdf5-joined = pkgs.symlinkJoin {
-          name = "hdf5";
-          paths = with pkgs; [hdf5 hdf5.dev];
-        };
-
         nativeBuildInputs = with pkgs; [
           cmake
           flatbuffers
-          hdf5-joined
           perl
           tcl
           pkg-config
         ];
         buildInputs = with pkgs; [
           openssl
           cyrus_sasl
-          hdf5-joined
         ];
 
         lintingRustFlags = "-D unused-crate-dependencies";
@@ -80,15 +70,14 @@
           ];
 
           RUSTFLAGS = lintingRustFlags;
-          HDF5_DIR = "${hdf5-joined}";
         };
 
         packages =
           import ./diagnostics {inherit pkgs naersk' version gitRevision nativeBuildInputs buildInputs;}
           // import ./digitiser-aggregator {inherit pkgs naersk' version gitRevision nativeBuildInputs buildInputs;}
-          // import ./nexus-writer {inherit pkgs naersk' version gitRevision nativeBuildInputs buildInputs hdf5-joined;}
+          // import ./nexus-writer {inherit pkgs naersk' version gitRevision nativeBuildInputs buildInputs;}
           // import ./simulator {inherit pkgs naersk' version gitRevision nativeBuildInputs buildInputs;}
-          // import ./trace-archiver-hdf5 {inherit pkgs naersk' version gitRevision nativeBuildInputs buildInputs hdf5-joined;}
+          // import ./trace-archiver-hdf5 {inherit pkgs naersk' version gitRevision nativeBuildInputs buildInputs;}
           // import ./trace-archiver-tdengine {inherit pkgs naersk' version gitRevision nativeBuildInputs buildInputs;}
           // import ./trace-reader {inherit pkgs naersk' version gitRevision nativeBuildInputs buildInputs;}
           // import ./trace-telemetry-exporter {inherit pkgs naersk' version gitRevision nativeBuildInputs buildInputs;}

nexus-writer/default.nix

@@ -5,7 +5,6 @@
   gitRevision,
   nativeBuildInputs,
   buildInputs,
-  hdf5-joined,
 }: rec {
   nexus-writer = naersk'.buildPackage {
     name = "nexus-writer";
@@ -20,8 +19,6 @@
     overrideMain = p: {
       GIT_REVISION = gitRevision;
     };
-
-    HDF5_DIR = "${hdf5-joined}";
   };
 
   nexus-writer-container-image = pkgs.dockerTools.buildImage {

trace-archiver-hdf5/default.nix

@@ -5,7 +5,6 @@
   gitRevision,
   nativeBuildInputs,
   buildInputs,
-  hdf5-joined,
 }: rec {
   trace-archiver-hdf5 = naersk'.buildPackage {
     name = "trace-archiver-hdf5";
@@ -20,8 +19,6 @@
     overrideMain = p: {
       GIT_REVISION = gitRevision;
     };
-
-    HDF5_DIR = "${hdf5-joined}";
   };
 
   trace-archiver-hdf5-container-image = pkgs.dockerTools.buildImage {