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

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

@@ -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

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

@@ -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

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

@@ -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

.gitmodules

@@ -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

configs/common/packages.yaml

@@ -374,6 +374,10 @@ packages:
     py-poetry-core:
       require:
       - '@1.7'
+    # Need at least py-pygithub@2.7 for self-hosted runner management
+    py-pygithub:
+      require:
+      - '@2.7:'
     # This version builds with Intel oneAPI compilers, newer versions don't
     py-pyogrio:
       require:
@@ -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

configs/common/packages_oneapi.yaml

@@ -32,6 +32,9 @@ packages:
     gmake:
       require:
       - '%gcc'
+    go:
+      require:
+      - '%c,cxx=gcc'
     libbsd:
       require:
       - '%gcc'

configs/sites/tier1/atlantis/packages.yaml

@@ -15,6 +15,10 @@ packages:
     externals:
     - spec: automake@1.16.1
       prefix: /usr
+  bash:
+    externals:
+    - spec: bash@4.4.20
+      prefix: /usr
   binutils:
     externals:
     - spec: binutils@2.30.117

configs/sites/tier1/blueback/packages.yaml

@@ -12,6 +12,10 @@ packages:
     externals:
     - spec: automake@1.15.1
       prefix: /usr
+  bash:
+    externals:
+    - spec: bash@4.4.23
+      prefix: /usr
   binutils:
     externals:
     - spec: binutils@2.43.1~gold+headers

configs/sites/tier1/narwhal/packages.yaml

@@ -12,6 +12,10 @@ packages:
     externals:
     - spec: automake@1.15.1
       prefix: /usr
+  bash:
+    externals:
+    - spec: bash@4.4.23
+      prefix: /usr
   binutils:
     externals:
     - spec: binutils@2.37.20211103

configs/sites/tier1/nautilus/packages.yaml

@@ -12,6 +12,10 @@ packages:
     externals:
     - spec: automake@1.16.1
       prefix: /usr
+  bash:
+    externals:
+    - spec: bash@4.4.20
+      prefix: /usr
   binutils:
     externals:
     - spec: binutils@2.30.117

configs/sites/tier2/blackpearl/packages.yaml

@@ -10,6 +10,10 @@ packages:
     externals:
     - spec: automake@1.16.2
       prefix: /usr
+  bash:
+    externals:
+    - spec: bash@5.1.8
+      prefix: /usr
   binutils:
     externals:
     - spec: binutils@2.35.2

configs/sites/tier2/bounty/packages.yaml

@@ -10,6 +10,10 @@ packages:
     externals:
     - spec: automake@1.16.2
       prefix: /usr
+  bash:
+    externals:
+    - spec: bash@5.1.8
+      prefix: /usr
   binutils:
     externals:
     - spec: binutils@2.35.2~gold+headers

configs/sites/tier2/jean/packages.yaml

@@ -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: zlib@1.2.11
-      prefix: /usr
-
-# All other packages listed alphabetically
-  autoconf:
-    externals:
-    - spec: autoconf@2.69
-      prefix: /usr
-  automake:
-    externals:
-    - spec: automake@1.16.1
-      prefix: /usr
-  binutils:
-    externals:
-    - spec: binutils@2.30.125~gold~headers
-      prefix: /usr
-  #bison:
-  #  externals:
-  #  - spec: bison@3.0.4
-  #    prefix: /usr
-  coreutils:
-    externals:
-    - spec: coreutils@8.30
-      prefix: /usr
-  #curl:
-  #  externals:
-  #  - spec: curl@7.61.1+gssapi+ldap+nghttp2
-  #    prefix: /usr
-  diffutils:
-    externals:
-    - spec: diffutils@3.6
-      prefix: /usr
-  findutils:
-    externals:
-    - spec: findutils@4.6.0
-      prefix: /usr
-  flex:
-    externals:
-    - spec: flex@2.6.1+lex
-      prefix: /usr
-  gawk:
-    externals:
-    - spec: gawk@4.2.1
-      prefix: /usr
-  gettext:
-    externals:
-    - spec: gettext@0.19.8.1
-      prefix: /usr
-  git:
-    externals:
-    - spec: git@2.43.5~tcltk
-      prefix: /usr
-  # DH* external git-lfs missing
-  groff:
-    externals:
-    - spec: groff@1.22.3
-      prefix: /usr
-  gmake:
-    externals:
-    - spec: gmake@4.2.1
-      prefix: /usr
-  libtool:
-    externals:
-    - spec: libtool@2.4.6
-      prefix: /usr
-  m4:
-    externals:
-    - spec: m4@1.4.18
-      prefix: /usr
-  openssh:
-    externals:
-    - spec: openssh@8.0p1
-      prefix: /usr
-    #- spec: openssh@10.0p2a
-    #  prefix: /usr/local/krb5
-  #openssl:
-  #  externals:
-  #  - spec: openssl@1.1.1k
-  #    prefix: /usr
-  #perl:
-  #  externals:
-  #  - spec: perl@5.26.3~cpanm+opcode+open+shared+threads
-  #    prefix: /usr
-  pkgconf:
-    externals:
-    - spec: pkgconf@1.4.2
-      prefix: /usr
-  # DH* external qt5 missing
-  sed:
-    externals:
-    - spec: sed@4.5
-      prefix: /usr
-  tar:
-    externals:
-    - spec: tar@1.30
-      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: zlib@1.2.11
+      prefix: /usr
+
+# All other packages listed alphabetically
+  autoconf:
+    externals:
+    - spec: autoconf@2.69
+      prefix: /usr
+  automake:
+    externals:
+    - spec: automake@1.16.1
+      prefix: /usr
+  bash:
+    externals:
+    - spec: bash@4.4.20
+      prefix: /usr
+  binutils:
+    externals:
+    - spec: binutils@2.30.125~gold~headers
+      prefix: /usr
+  #bison:
+  #  externals:
+  #  - spec: bison@3.0.4
+  #    prefix: /usr
+  coreutils:
+    externals:
+    - spec: coreutils@8.30
+      prefix: /usr
+  #curl:
+  #  externals:
+  #  - spec: curl@7.61.1+gssapi+ldap+nghttp2
+  #    prefix: /usr
+  diffutils:
+    externals:
+    - spec: diffutils@3.6
+      prefix: /usr
+  findutils:
+    externals:
+    - spec: findutils@4.6.0
+      prefix: /usr
+  flex:
+    externals:
+    - spec: flex@2.6.1+lex
+      prefix: /usr
+  gawk:
+    externals:
+    - spec: gawk@4.2.1
+      prefix: /usr
+  gettext:
+    externals:
+    - spec: gettext@0.19.8.1
+      prefix: /usr
+  git:
+    externals:
+    - spec: git@2.43.5~tcltk
+      prefix: /usr
+  # DH* external git-lfs missing
+  groff:
+    externals:
+    - spec: groff@1.22.3
+      prefix: /usr
+  gmake:
+    externals:
+    - spec: gmake@4.2.1
+      prefix: /usr
+  libtool:
+    externals:
+    - spec: libtool@2.4.6
+      prefix: /usr
+  m4:
+    externals:
+    - spec: m4@1.4.18
+      prefix: /usr
+  openssh:
+    externals:
+    - spec: openssh@8.0p1
+      prefix: /usr
+    #- spec: openssh@10.0p2a
+    #  prefix: /usr/local/krb5
+  #openssl:
+  #  externals:
+  #  - spec: openssl@1.1.1k
+  #    prefix: /usr
+  #perl:
+  #  externals:
+  #  - spec: perl@5.26.3~cpanm+opcode+open+shared+threads
+  #    prefix: /usr
+  pkgconf:
+    externals:
+    - spec: pkgconf@1.4.2
+      prefix: /usr
+  # DH* external qt5 missing
+  sed:
+    externals:
+    - spec: sed@4.5
+      prefix: /usr
+  tar:
+    externals:
+    - spec: tar@1.30
+      prefix: /usr

configs/sites/tier2/wheat/packages.yaml

@@ -21,6 +21,10 @@ packages:
     externals:
     - spec: automake@1.16.1
       prefix: /usr
+  bash:
+    externals:
+    - spec: bash@4.4.20
+      prefix: /usr
   binutils:
     externals:
     - spec: binutils@2.30.117

configs/templates/neptune-dev/spack.yaml

@@ -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
   - crtm@3.1.2
   - crtm@v2.4.1-jedi.2
 

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

@@ -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.