Add gittools as varant to neptune-python-env/neptune-dev, add rank-run to base-env #1891

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Merged

climbfuji merged 8 commits into JCSDA:develop from climbfuji:feature/neptune_env_gittools

Jan 28, 2026

.github/workflows/ubuntu-ci-x86_64-gnu.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -101,6 +101,7 @@ jobs: @@
                 spack external find --scope system wget
                 spack external find --scope system texlive
                 spack external find --scope system mysql
+                spack external find --scope system bash
                 # Find compilers
                 spack compiler find --scope system
@@ Expand Down @@

.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -101,6 +101,7 @@ jobs: @@
                 spack external find --scope system wget
                 spack external find --scope system texlive
                 spack external find --scope system mysql
+                spack external find --scope system bash
                 # Find compilers
                 spack compiler find --scope system
@@ Expand Down @@

.github/workflows/ubuntu-ci-x86_64-oneapi.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -101,6 +101,7 @@ jobs: @@
                 spack external find --scope system wget
                 spack external find --scope system texlive
                 spack external find --scope system mysql
+                spack external find --scope system bash
                 # Find compilers
                 spack compiler find --scope system
@@ Expand Down @@

.gitmodules

-Original file line number
+Diff line change
@@ -1,9 +1,7 @@
     [submodule "spack"]
       path = spack
-      #url = https://github.com/jcsda/spack
-      #branch = spack-stack-dev
-      url = https://github.com/climbfuji/spack
-      branch = feature/update_spack-stack-dev_from_develop
+      url = https://github.com/jcsda/spack
+      branch = spack-stack-dev
     [submodule "repos/builtin"]
       path = repos/builtin
       url = https://github.com/jcsda/spack-packages
@@ Expand Down @@

configs/common/packages.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -374,6 +374,10 @@ packages: @@
         py-poetry-core:
           require:
           - '@1.7'
+        # Need at least [email protected] for self-hosted runner management
+        py-pygithub:
+          require:
+          - '@2.7:'
         # This version builds with Intel oneAPI compilers, newer versions don't
         py-pyogrio:
           require:
@@ Expand All / @@ -394,7 +398,6 @@ packages: @@
         py-setuptools:
           require:
           - '@69'
-        ## When making changes here, also check the packages.yaml for atlantis, nautilus, blackpearl
         py-torch:
           require:
           - +custom-protobuf ~mkldnn
@@ Expand Down @@

configs/common/packages_oneapi.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -32,6 +32,9 @@ packages: @@
         gmake:
           require:
           - '%gcc'
+        go:
+          require:
+          - '%c,cxx=gcc'
         libbsd:
           require:
           - '%gcc'
@@ Expand Down @@

configs/sites/tier1/atlantis/packages.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -15,6 +15,10 @@ packages: @@
         externals:
         - spec: [email protected]
           prefix: /usr
+      bash:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
       binutils:
         externals:
         - spec: [email protected]
@@ Expand Down @@

configs/sites/tier1/blueback/packages.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -12,6 +12,10 @@ packages: @@
         externals:
         - spec: [email protected]
           prefix: /usr
+      bash:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
       binutils:
         externals:
         - spec: [email protected]~gold+headers
@@ Expand Down @@

configs/sites/tier1/narwhal/packages.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -12,6 +12,10 @@ packages: @@
         externals:
         - spec: [email protected]
           prefix: /usr
+      bash:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
       binutils:
         externals:
         - spec: [email protected]
@@ Expand Down @@

configs/sites/tier1/nautilus/packages.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -12,6 +12,10 @@ packages: @@
         externals:
         - spec: [email protected]
           prefix: /usr
+      bash:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
       binutils:
         externals:
         - spec: [email protected]
@@ Expand Down @@

configs/sites/tier2/blackpearl/packages.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -10,6 +10,10 @@ packages: @@
         externals:
         - spec: [email protected]
           prefix: /usr
+      bash:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
       binutils:
         externals:
         - spec: [email protected]
@@ Expand Down @@

configs/sites/tier2/bounty/packages.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -10,6 +10,10 @@ packages: @@
         externals:
         - spec: [email protected]
           prefix: /usr
+      bash:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
       binutils:
         externals:
         - spec: [email protected]~gold+headers
@@ Expand Down @@

configs/sites/tier2/jean/packages.yaml

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-Original file line number
+Diff line change
@@ -1,107 +1,111 @@
-    packages:
-      # Modification of common packages
-      # Use system zlib instead of spack-built zlib-ng
-      all:
-        providers:
-          zlib-api:: [zlib]
-      zlib-api:
-        buildable: False
-      zlib:
-        buildable: False
-        externals:
-        - spec: [email protected]
-          prefix: /usr
-    # All other packages listed alphabetically
-      autoconf:
-        externals:
-        - spec: [email protected]
-          prefix: /usr
-      automake:
-        externals:
-        - spec: [email protected]
-          prefix: /usr
-      binutils:
-        externals:
-        - spec: [email protected]~gold~headers
-          prefix: /usr
-      #bison:
-      #  externals:
-      #  - spec: [email protected]
-      #    prefix: /usr
-      coreutils:
-        externals:
-        - spec: [email protected]
-          prefix: /usr
-      #curl:
-      #  externals:
-      #  - spec: [email protected]+gssapi+ldap+nghttp2
-      #    prefix: /usr
-      diffutils:
-        externals:
-        - spec: [email protected]
-          prefix: /usr
-      findutils:
-        externals:
-        - spec: [email protected]
-          prefix: /usr
-      flex:
-        externals:
-        - spec: [email protected]+lex
-          prefix: /usr
-      gawk:
-        externals:
-        - spec: [email protected]
-          prefix: /usr
-      gettext:
-        externals:
-        - spec: [email protected]
-          prefix: /usr
-      git:
-        externals:
-        - spec: [email protected]~tcltk
-          prefix: /usr
-      # DH* external git-lfs missing
-      groff:
-        externals:
-        - spec: [email protected]
-          prefix: /usr
-      gmake:
-        externals:
-        - spec: [email protected]
-          prefix: /usr
-      libtool:
-        externals:
-        - spec: [email protected]
-          prefix: /usr
-      m4:
-        externals:
-        - spec: [email protected]
-          prefix: /usr
-      openssh:
-        externals:
-        - spec: [email protected]
-          prefix: /usr
-        #- spec: [email protected]
-        #  prefix: /usr/local/krb5
-      #openssl:
-      #  externals:
-      #  - spec: [email protected]
-      #    prefix: /usr
-      #perl:
-      #  externals:
-      #  - spec: [email protected]~cpanm+opcode+open+shared+threads
-      #    prefix: /usr
-      pkgconf:
-        externals:
-        - spec: [email protected]
-          prefix: /usr
-      # DH* external qt5 missing
-      sed:
-        externals:
-        - spec: [email protected]
-          prefix: /usr
-      tar:
-        externals:
-        - spec: [email protected]
-          prefix: /usr
+    packages:
+      # Modification of common packages
+      # Use system zlib instead of spack-built zlib-ng
+      all:
+        providers:
+          zlib-api:: [zlib]
+      zlib-api:
+        buildable: False
+      zlib:
+        buildable: False
+        externals:
+        - spec: [email protected]
+          prefix: /usr
+    # All other packages listed alphabetically
+      autoconf:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
+      automake:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
+      bash:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
+      binutils:
+        externals:
+        - spec: [email protected]~gold~headers
+          prefix: /usr
+      #bison:
+      #  externals:
+      #  - spec: [email protected]
+      #    prefix: /usr
+      coreutils:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
+      #curl:
+      #  externals:
+      #  - spec: [email protected]+gssapi+ldap+nghttp2
+      #    prefix: /usr
+      diffutils:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
+      findutils:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
+      flex:
+        externals:
+        - spec: [email protected]+lex
+          prefix: /usr
+      gawk:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
+      gettext:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
+      git:
+        externals:
+        - spec: [email protected]~tcltk
+          prefix: /usr
+      # DH* external git-lfs missing
+      groff:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
+      gmake:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
+      libtool:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
+      m4:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
+      openssh:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
+        #- spec: [email protected]
+        #  prefix: /usr/local/krb5
+      #openssl:
+      #  externals:
+      #  - spec: [email protected]
+      #    prefix: /usr
+      #perl:
+      #  externals:
+      #  - spec: [email protected]~cpanm+opcode+open+shared+threads
+      #    prefix: /usr
+      pkgconf:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
+      # DH* external qt5 missing
+      sed:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
+      tar:
+        externals:
+        - spec: [email protected]
+          prefix: /usr

configs/sites/tier2/wheat/packages.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -21,6 +21,10 @@ packages: @@
         externals:
         - spec: [email protected]
           prefix: /usr
+      bash:
+        externals:
+        - spec: [email protected]
+          prefix: /usr
       binutils:
         externals:
         - spec: [email protected]
@@ Expand Down @@

configs/templates/neptune-dev/spack.yaml

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -12,8 +12,8 @@ spack:
  
      - neptune-env +debug +openmp +espc +ncview ^esmf@=8.9.1

      - neptune-env ~debug ~openmp +espc +ncview ^esmf@=8.9.1

      - neptune-env +debug ~openmp +espc +ncview ^esmf@=8.9.1

      - neptune-python-env    ^neptune-env ~debug +openmp +espc +ncview ^esmf@=8.9.1

      - jedi-neptune-env +adp ^neptune-env ~debug +openmp +espc +ncview ^esmf@=8.9.1

      - neptune-python-env +gittools ^neptune-env ~debug +openmp +espc +ncview ^esmf@=8.9.1

      - jedi-neptune-env +adp        ^neptune-env ~debug +openmp +espc +ncview ^esmf@=8.9.1

      - [email protected]

      - [email protected]

repos/builtin

Submodule builtin updated 2 files

+15 −1		repos/spack_repo/builtin/packages/py_pygithub/package.py
+26 −0		repos/spack_repo/builtin/packages/rank_run/package.py

repos/spack_stack/spack_repo/spack_stack/packages/base_env/package.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -44,4 +44,7 @@ class BaseEnv(BundlePackage): @@
         depends_on("py-setuptools-scm", type="run")
         depends_on("py-pytest", type="run")
+        # Miscellaneous
+        depends_on("rank-run", type="run")
         # There is no need for install() since there is no code.

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Add gittools as varant to neptune-python-env/neptune-dev, add rank-run to base-env #1891

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