From c71ac440a1e7358b55891daea46d5520f62eb56d Mon Sep 17 00:00:00 2001
From: aprozo <alexandr.a.prozorov@gmail.com>
Date: Fri, 17 Jul 2026 12:01:16 +0100
Subject: [PATCH 1/9] feat: install the EIC MCP server stack via spack packages

The eic-mcp launcher and every MCP server now come from eic-spack recipes
and land in /opt/local/bin via the environment view (supersedes #328: no
bundled script, no runtime clone/build).

- xl/spack.yaml: add eic-mcp, rucio-eic-mcp-server, supergateway,
  uproot-mcp-server (xrootd-/zenodo-mcp-server were already in)
- packages.yaml: version requires for the servers and bridge; py-mcp +cli
---
 spack-environment/packages.yaml | 22 ++++++++++++++++++++++
 spack-environment/xl/spack.yaml |  4 ++++
 2 files changed, 26 insertions(+)

diff --git a/spack-environment/packages.yaml b/spack-environment/packages.yaml
index c309dc421..84686aea7 100644
--- a/spack-environment/packages.yaml
+++ b/spack-environment/packages.yaml
@@ -158,6 +158,9 @@ packages:
     externals:
     - spec: egl@1.5.0
       prefix: /usr
+  eic-mcp:
+    require:
+    - '@main'  # pin to the first tagged release once eic/eic-mcp tags one
   eic-opticks:
     require:
     - '@0.3.0'
@@ -510,6 +513,10 @@ packages:
   py-matplotlib:
     require:
     - '@3.10'  # avoid FT_Render_Glyph errors possibly due to https://github.com/matplotlib/matplotlib/pull/30059
+  py-mcp:
+    require:
+    - '@1.28:'
+    - +cli  # rucio-eic-mcp-server needs mcp[cli]
   py-mplhep:
     require:
     - '@0.4.0:'
@@ -622,6 +629,9 @@ packages:
     - '@6.38.04'
     - cxxstd=20 +fftw +fortran +gdml +http -ipo +mlp +python +root7 +tmva +tmva-sofie +x +xrootd +ssl
     - any_of: [+opengl +webgui, -opengl -webgui]
+  rucio-eic-mcp-server:
+    require:
+    - '@0.1.0:'
   sherpa:
     require:
     - '@3.0.1'
@@ -665,6 +675,9 @@ packages:
   strace:
     require:
     - -mpers
+  supergateway:
+    require:
+    - '@3.4.3:'
   swig:
     require:
     - '@4.1:'  # constrain to avoid duplicates in eic_tf
@@ -675,6 +688,9 @@ packages:
     require:
     - '@2.8.0'
     - -xnnpack
+  uproot-mcp-server:
+    require:
+    - '@0.1.0:'
   valgrind:
     require:
     - '@3.20.0:'
@@ -688,9 +704,15 @@ packages:
     require:
     - '@5.7.0:'
     - cxxstd=20 -davix +python +scitokens-cpp
+  xrootd-mcp-server:
+    require:
+    - '@0.1.0:'
   yoda:
     require:
     - '@2.1.0:'
+  zenodo-mcp-server:
+    require:
+    - '@0.1.0:'
   zlib-api:
     require:
     - zlib-ng
diff --git a/spack-environment/xl/spack.yaml b/spack-environment/xl/spack.yaml
index 474c392ac..576a90eff 100644
--- a/spack-environment/xl/spack.yaml
+++ b/spack-environment/xl/spack.yaml
@@ -28,6 +28,7 @@ spack:
   - doxygen
   - east
   - edm4hep
+  - eic-mcp
   - eic-smear
   - eigen
   - emacs
@@ -126,6 +127,7 @@ spack:
   - py-yapf
   - rivet
   - root
+  - rucio-eic-mcp-server
   - sherpa
   - simsipm
   - slurm sysconfdir=/etc/slurm
@@ -133,6 +135,8 @@ spack:
   - spdlog
   - stow
   - strace
+  - supergateway
+  - uproot-mcp-server
   - valgrind
   - xeyes
   - xrootd

From 95e1fbb2664822d226f6c3069be4e455034b2558 Mon Sep 17 00:00:00 2001
From: aprozo <alexandr.a.prozorov@gmail.com>
Date: Fri, 17 Jul 2026 12:01:16 +0100
Subject: [PATCH 2/9] feat: opencode, an AI coding agent CLI

For headless LLM-client use inside eic-shell (farm nodes, CI reproducers).
Installed from the per-platform GitHub release binary.
---
 spack-environment/packages.yaml | 3 +++
 spack-environment/xl/spack.yaml | 1 +
 2 files changed, 4 insertions(+)

diff --git a/spack-environment/packages.yaml b/spack-environment/packages.yaml
index 84686aea7..cb9662c4f 100644
--- a/spack-environment/packages.yaml
+++ b/spack-environment/packages.yaml
@@ -383,6 +383,9 @@ packages:
     require:
     - '@7.8.1:'
     - +application_framework -vtk
+  opencode:
+    require:
+    - '@1.18.3:'
   opengl:
     buildable: False
     externals:
diff --git a/spack-environment/xl/spack.yaml b/spack-environment/xl/spack.yaml
index 576a90eff..ec4624f2c 100644
--- a/spack-environment/xl/spack.yaml
+++ b/spack-environment/xl/spack.yaml
@@ -70,6 +70,7 @@ spack:
   - ollama
   - onnx
   - opencascade
+  - opencode
   - osg-ca-certs
   - pelican
   - phonebook-cli

From 359fad94af1be30699db5a7c43a13ce8aeea1008 Mon Sep 17 00:00:00 2001
From: aprozo <alexandr.a.prozorov@gmail.com>
Date: Fri, 17 Jul 2026 12:01:16 +0100
Subject: [PATCH 3/9] chore: TESTING pin eic-spack to the MCP recipes branch

Points at aprozo/eic-spack feat/mcp-servers (develop@dd8a73e + the new
recipes). Revert to eic/eic-spack at the merge SHA before undrafting.
---
 eic-spack.sh | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/eic-spack.sh b/eic-spack.sh
index dca91197a..81a1ea559 100644
--- a/eic-spack.sh
+++ b/eic-spack.sh
@@ -1,8 +1,10 @@
 # shellcheck shell=bash
 # shellcheck disable=SC2034  # Variables are used by scripts that source this file
 ## EIC spack organization and repository, e.g. eic/eic-spack
-EICSPACK_ORGREPO="eic/eic-spack"
+## TESTING ONLY — revert to eic/eic-spack + the merge SHA before undrafting.
+## The pinned commit is develop@dd8a73e + the MCP/opencode recipes.
+EICSPACK_ORGREPO="aprozo/eic-spack"
 
 ## EIC spack commit hash or github version, e.g. v0.19.7
 ## note: nightly builds could use a branch e.g. releases/v0.19
-EICSPACK_VERSION="dd8a73e348ec36c685da707c2d33f1d94b8df82c"
+EICSPACK_VERSION="f356d6b81a19173901ef1e68eb2bb59099610b5f"

From ce2fcba7936d7ce89074c78ff5b146d92500b418 Mon Sep 17 00:00:00 2001
From: aprozo <alexandr.a.prozorov@gmail.com>
Date: Fri, 17 Jul 2026 14:20:37 +0100
Subject: [PATCH 4/9] fix: py-mcp without the cli variant

py-typer (newest builtin: 0.23.2) pins py-click@:8.1.8, which cannot unify
with the environment's click 8.3+ (flask via pyrobird). The MCP servers
only need mcp core, so the eic-spack recipes default the cli variant off.
---
 spack-environment/packages.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/spack-environment/packages.yaml b/spack-environment/packages.yaml
index cb9662c4f..9321670ad 100644
--- a/spack-environment/packages.yaml
+++ b/spack-environment/packages.yaml
@@ -519,7 +519,8 @@ packages:
   py-mcp:
     require:
     - '@1.28:'
-    - +cli  # rucio-eic-mcp-server needs mcp[cli]
+    # no +cli: the typer-based mcp CLI pins py-click@:8.1.8, which cannot
+    # unify with the environment's click 8.3+ (flask); servers need mcp core
   py-mplhep:
     require:
     - '@0.4.0:'

From 3d658cc8888863f3e9c634ac5e3d868c71ac401c Mon Sep 17 00:00:00 2001
From: aprozo <alexandr.a.prozorov@gmail.com>
Date: Fri, 17 Jul 2026 17:39:31 +0100
Subject: [PATCH 5/9] chore: bump the TESTING eic-spack pin to the current #986
 head

The previous pin predated py-mcp defaulting ~cli, so the typer/click
conflict was still in the DAG. Also picks up the py-pyjwt import-test
path fix, and drops the fork indirection now that the branch lives on
eic/eic-spack.
---
 eic-spack.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/eic-spack.sh b/eic-spack.sh
index 81a1ea559..b64235246 100644
--- a/eic-spack.sh
+++ b/eic-spack.sh
@@ -1,10 +1,10 @@
 # shellcheck shell=bash
 # shellcheck disable=SC2034  # Variables are used by scripts that source this file
 ## EIC spack organization and repository, e.g. eic/eic-spack
-## TESTING ONLY — revert to eic/eic-spack + the merge SHA before undrafting.
-## The pinned commit is develop@dd8a73e + the MCP/opencode recipes.
-EICSPACK_ORGREPO="aprozo/eic-spack"
+EICSPACK_ORGREPO="eic/eic-spack"
 
 ## EIC spack commit hash or github version, e.g. v0.19.7
 ## note: nightly builds could use a branch e.g. releases/v0.19
-EICSPACK_VERSION="f356d6b81a19173901ef1e68eb2bb59099610b5f"
+## TESTING: head of eic-spack#986 (develop@dd8a73e + the MCP/opencode
+## recipes); bump to the merge SHA before undrafting.
+EICSPACK_VERSION="44bb45e3d8874740410d7152ce8f778893dcb86b"

From 33e227bcfdc19255bcda86bc31ef8de36447c9fc Mon Sep 17 00:00:00 2001
From: aprozo <alexandr.a.prozorov@gmail.com>
Date: Mon, 31 Aug 2026 12:14:16 +0200
Subject: [PATCH 6/9] xl: drop supergateway; track main for the native-HTTP MCP
 servers
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The MCP servers now speak streamable HTTP themselves and eic-mcp starts
them directly, so the stdio bridge is gone from the environment.  The three
server pins move to '@main' — the only pin that builds before the v0.2.0
tags exist — mirroring the precedent eic-mcp already sets; flip them to
'@0.2.0:' once the tags are pushed (grep TODO(push)).
---
 eic-spack.sh                    | 1 +
 spack-environment/packages.yaml | 9 +++------
 spack-environment/xl/spack.yaml | 1 -
 3 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/eic-spack.sh b/eic-spack.sh
index b64235246..cb3ace1ef 100644
--- a/eic-spack.sh
+++ b/eic-spack.sh
@@ -7,4 +7,5 @@ EICSPACK_ORGREPO="eic/eic-spack"
 ## note: nightly builds could use a branch e.g. releases/v0.19
 ## TESTING: head of eic-spack#986 (develop@dd8a73e + the MCP/opencode
 ## recipes); bump to the merge SHA before undrafting.
+## TODO(push): bump to the new feat/mcp-servers head (native HTTP, no supergateway).
 EICSPACK_VERSION="44bb45e3d8874740410d7152ce8f778893dcb86b"
diff --git a/spack-environment/packages.yaml b/spack-environment/packages.yaml
index 9321670ad..81a58bbd5 100644
--- a/spack-environment/packages.yaml
+++ b/spack-environment/packages.yaml
@@ -635,7 +635,7 @@ packages:
     - any_of: [+opengl +webgui, -opengl -webgui]
   rucio-eic-mcp-server:
     require:
-    - '@0.1.0:'
+    - '@main'  # native streamable HTTP; pin to '@0.2.0:' once v0.2.0 is tagged
   sherpa:
     require:
     - '@3.0.1'
@@ -679,9 +679,6 @@ packages:
   strace:
     require:
     - -mpers
-  supergateway:
-    require:
-    - '@3.4.3:'
   swig:
     require:
     - '@4.1:'  # constrain to avoid duplicates in eic_tf
@@ -694,7 +691,7 @@ packages:
     - -xnnpack
   uproot-mcp-server:
     require:
-    - '@0.1.0:'
+    - '@main'  # native streamable HTTP; pin to '@0.2.0:' once v0.2.0 is tagged
   valgrind:
     require:
     - '@3.20.0:'
@@ -710,7 +707,7 @@ packages:
     - cxxstd=20 -davix +python +scitokens-cpp
   xrootd-mcp-server:
     require:
-    - '@0.1.0:'
+    - '@main'  # native streamable HTTP; pin to '@0.2.0:' once v0.2.0 is tagged
   yoda:
     require:
     - '@2.1.0:'
diff --git a/spack-environment/xl/spack.yaml b/spack-environment/xl/spack.yaml
index ec4624f2c..ce6ca41bd 100644
--- a/spack-environment/xl/spack.yaml
+++ b/spack-environment/xl/spack.yaml
@@ -136,7 +136,6 @@ spack:
   - spdlog
   - stow
   - strace
-  - supergateway
   - uproot-mcp-server
   - valgrind
   - xeyes

From e0bc4d153843604fad5f558c04774c1f9e0b763b Mon Sep 17 00:00:00 2001
From: aprozo <alexandr.a.prozorov@gmail.com>
Date: Mon, 31 Aug 2026 14:24:08 +0200
Subject: [PATCH 7/9] =?UTF-8?q?xl:=20drop=20opencode=20=E2=80=94=20it=20st?=
 =?UTF-8?q?ays=20a=20host-side=20install?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 spack-environment/packages.yaml | 3 ---
 spack-environment/xl/spack.yaml | 1 -
 2 files changed, 4 deletions(-)

diff --git a/spack-environment/packages.yaml b/spack-environment/packages.yaml
index 81a58bbd5..40be316eb 100644
--- a/spack-environment/packages.yaml
+++ b/spack-environment/packages.yaml
@@ -383,9 +383,6 @@ packages:
     require:
     - '@7.8.1:'
     - +application_framework -vtk
-  opencode:
-    require:
-    - '@1.18.3:'
   opengl:
     buildable: False
     externals:
diff --git a/spack-environment/xl/spack.yaml b/spack-environment/xl/spack.yaml
index ce6ca41bd..eca693d24 100644
--- a/spack-environment/xl/spack.yaml
+++ b/spack-environment/xl/spack.yaml
@@ -70,7 +70,6 @@ spack:
   - ollama
   - onnx
   - opencascade
-  - opencode
   - osg-ca-certs
   - pelican
   - phonebook-cli

From ce4d0b860e0b59c3580b15120f737f1a8177b633 Mon Sep 17 00:00:00 2001
From: aprozo <alexandr.a.prozorov@gmail.com>
Date: Mon, 31 Aug 2026 15:13:14 +0200
Subject: [PATCH 8/9] cherry-pick spack-packages#5637 (py-mcp + deps); track
 the deduped eic-spack head

---
 eic-spack.sh      | 5 +++--
 spack-packages.sh | 2 ++
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/eic-spack.sh b/eic-spack.sh
index cb3ace1ef..2af0355e4 100644
--- a/eic-spack.sh
+++ b/eic-spack.sh
@@ -7,5 +7,6 @@ EICSPACK_ORGREPO="eic/eic-spack"
 ## note: nightly builds could use a branch e.g. releases/v0.19
 ## TESTING: head of eic-spack#986 (develop@dd8a73e + the MCP/opencode
 ## recipes); bump to the merge SHA before undrafting.
-## TODO(push): bump to the new feat/mcp-servers head (native HTTP, no supergateway).
-EICSPACK_VERSION="44bb45e3d8874740410d7152ce8f778893dcb86b"
+## TESTING: head of eic-spack#986 (native HTTP, no supergateway, py-* deps
+## from the spack-packages#5637 cherry-pick); bump to the merge SHA before undrafting.
+EICSPACK_VERSION="646ef8ccdd18ba3c69b91331c08dd50e4715210d"
diff --git a/spack-packages.sh b/spack-packages.sh
index 09cf311c2..c2c8fa92a 100644
--- a/spack-packages.sh
+++ b/spack-packages.sh
@@ -23,6 +23,7 @@ a7c32f24cd5b69b237dc974804a71326306f4e58
 de97f131df3dbc940151f406afd5c2c1158a660c
 caf013be0ee1594fdbba8feb07ffecc88474a2b0
 75395349957ad785cca50002dffb18bbcb48af27
+d18c9ad43ea50d71e666c8a859da3293e4776c19
 ---
 ## Optional hash table with comma-separated file list
 ## For these commits, the cherry-pick will be restricted to the listed files only.
@@ -43,3 +44,4 @@ read -r -d '' SPACKPACKAGES_CHERRYPICKS_FILES <<- \
 ## de97f131df3dbc940151f406afd5c2c1158a660c: TensorFlow: add v2.21.0
 ## caf013be0ee1594fdbba8feb07ffecc88474a2b0: Add missing xxd dep
 ## 75395349957ad785cca50002dffb18bbcb48af27: py-torch: ensure setuptools is not unnecessarily constrained for 2.10:
+## d18c9ad43ea50d71e666c8a859da3293e4776c19: py-mcp: new package (with missing deps, py-pyjwt 2.10.1) (#5637)

From 6f7864db631267da035607a76a751bbb099a98b0 Mon Sep 17 00:00:00 2001
From: aprozo <alexandr.a.prozorov@gmail.com>
Date: Mon, 31 Aug 2026 15:29:26 +0200
Subject: [PATCH 9/9] xl: opencode via the upstream spack-packages recipe
 (#5639 cherry-pick)

Both picks (#5637, #5639) verified to apply cleanly in sequence onto
v2026.06.0.
---
 spack-environment/packages.yaml | 3 +++
 spack-environment/xl/spack.yaml | 1 +
 spack-packages.sh               | 2 ++
 3 files changed, 6 insertions(+)

diff --git a/spack-environment/packages.yaml b/spack-environment/packages.yaml
index a97737059..fc3df1b50 100644
--- a/spack-environment/packages.yaml
+++ b/spack-environment/packages.yaml
@@ -401,6 +401,9 @@ packages:
   opencascade:
     require:
     - '@7.8.1:'
+  opencode:
+    require:
+    - '@1.18.3:'
     - +application_framework -vtk
   opengl:
     buildable: False
diff --git a/spack-environment/xl/spack.yaml b/spack-environment/xl/spack.yaml
index af83114db..dd730cc0e 100644
--- a/spack-environment/xl/spack.yaml
+++ b/spack-environment/xl/spack.yaml
@@ -70,6 +70,7 @@ spack:
   - ollama
   - onnx
   - opencascade
+  - opencode
   - osg-ca-certs
   - pandorasdk
   - pelican
diff --git a/spack-packages.sh b/spack-packages.sh
index f16e40afc..bd283ea20 100644
--- a/spack-packages.sh
+++ b/spack-packages.sh
@@ -46,6 +46,7 @@ c44cd71db91d6e6c68cb604dcb87311b49b1bedb
 409826414a2221be56011f8f0f912905dae558cd
 63b8b9c3ac8ddcb2b9aafcd8160ff33bd6210f51
 d18c9ad43ea50d71e666c8a859da3293e4776c19
+55be3f79a559d1e8f5ae8dffd1516569f444b5d0
 ---
 ## Optional hash table with comma-separated file list
 ## For these commits, the cherry-pick will be restricted to the listed files only.
@@ -89,3 +90,4 @@ read -r -d '' SPACKPACKAGES_CHERRYPICKS_FILES <<- \
 ## 409826414a2221be56011f8f0f912905dae558cd: podio: Add version 1.8 and new parquet variant
 ## 63b8b9c3ac8ddcb2b9aafcd8160ff33bd6210f51: edm4hep: patch for new podio arrow targets
 ## d18c9ad43ea50d71e666c8a859da3293e4776c19: py-mcp: new package (with missing deps, py-pyjwt 2.10.1) (#5637)
+## 55be3f79a559d1e8f5ae8dffd1516569f444b5d0: opencode, bun: new packages (#5639)