Merge remote-tracking branch 'ESCOMP/cam_development' into rrtmgp-sw

Author: peverwhee

.github/workflows/fleximod_test.yaml

@@ -13,7 +13,7 @@ jobs:
         uses: actions/checkout@v4
       - id: run-fleximod
         run: |
-          $GITHUB_WORKSPACE/bin/git-fleximod update
+          $GITHUB_WORKSPACE/bin/git-fleximod update -o
           echo
           echo "Update complete, checking status"
           echo
@@ -23,7 +23,7 @@ jobs:
           echo
           echo "Checking if git fleximod matches expected externals"
           echo
-          git diff --exit-code
+          git add . && git diff --exit-code && git diff --cached --exit-code
 #      - name: Setup tmate session
 #        if: ${{ failure() }}
 #        uses: mxschmitt/action-tmate@v3

.gitmodules

@@ -110,56 +110,56 @@
 [submodule "cism"]
 path = components/cism
 url = https://github.com/ESCOMP/CISM-wrapper
-fxtag = cismwrap_2_2_006
+fxtag = cismwrap_2_2_010
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
 
 [submodule "rtm"]
 path = components/rtm
 url = https://github.com/ESCOMP/RTM
-fxtag = rtm1_0_86
+fxtag = rtm1_0_89
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/RTM
 
 [submodule "mosart"]
 path = components/mosart
 url = https://github.com/ESCOMP/MOSART
-fxtag = mosart1.1.08
+fxtag = mosart1.1.12
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
 
 [submodule "mizuRoute"]
 path = components/mizuRoute
 url = https://github.com/ESCOMP/mizuRoute
-fxtag = cesm-coupling.n03_v2.2.0
+fxtag = v3.0.0
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm1.0.53
+fxtag = ccs_config_cesm1.0.61
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.102
+fxtag = cime6.1.126
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
 [submodule "cmeps"]
 path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
-fxtag = cmeps1.0.47
+fxtag = cmeps1.1.16
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.73
+fxtag = cdeps1.0.80
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 
@@ -173,7 +173,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
 [submodule "parallelio"]
 path = libraries/parallelio
 url = https://github.com/NCAR/ParallelIO
-fxtag = pio2_6_4
+fxtag = pio2_6_6
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
 
@@ -187,7 +187,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CESM_CICE
 [submodule "clm"]
 path = components/clm
 url = https://github.com/ESCOMP/CTSM
-fxtag = ctsm5.3.029
+fxtag = alpha-ctsm5.4.CMIP7.09.ctsm5.3.068
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CTSM
 
@@ -201,7 +201,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/FMS_interface
 [submodule "tools/CUPiD"]
 path = tools/CUPiD
 url = https://github.com/NCAR/CUPiD.git
-fxtag = v0.2.1
+fxtag = v0.3.1
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/NCAR/CUPiD.git
 

.lib/git_fleximod/cli.py

@@ -1,9 +1,8 @@
 from pathlib import Path
 import argparse, os, sys
-from importlib.resources import files
 from git_fleximod import utils
 
-__version__ = "1.0.1"
+__version__ = "1.0.2"
 
 class CustomArgumentParser(argparse.ArgumentParser):
     def print_help(self, file=None):
@@ -12,8 +11,8 @@ def print_help(self, file=None):
 
         # Then append the contents of README.md
         candidate_paths = [
-            os.path.join(sys.prefix, "share", "your-package", "README.md"),
-            os.path.join(os.path.dirname(__file__), "..", "README.md")  # fallback for dev
+            Path(sys.prefix) / "share" / "git_fleximod" / "README.md",
+            Path(__file__).resolve().parent.parent / "README.md",  # fallback for dev
         ]
         for path in candidate_paths:
             if os.path.exists(path):
@@ -25,26 +24,21 @@ def print_help(self, file=None):
 def find_root_dir(filename=".gitmodules"):
     """ finds the highest directory in tree
     which contains a file called filename """
-    try:
-        root = utils.execute_subprocess(["git","rev-parse", "--show-toplevel"],
-                                        output_to_caller=True ).rstrip()
-    except:
-        d = Path.cwd()
-        root = Path(d.root)
-        dirlist = []
-        dl = d
-        while dl != root:
-            dirlist.append(dl)
-            dl = dl.parent
-        dirlist.append(root)
-        dirlist.reverse()
-
-        for dl in dirlist:
-            attempt = dl / filename
-            if attempt.is_file():
-                return str(dl)
-        return None
-    return Path(root)
+    d = Path.cwd()
+    root = Path(d.root)
+    dirlist = []
+    dl = d
+    while dl != root:
+        dirlist.append(dl)
+        dl = dl.parent
+    dirlist.append(root)
+    dirlist.reverse()
+
+    for dl in dirlist:
+        attempt = dl / filename
+        if attempt.is_file():
+            return str(dl)
+    return None
 
 def get_parser():
     description = """

.lib/git_fleximod/gitinterface.py

@@ -60,7 +60,14 @@ def _git_operation_command(self, operation, args):
 
     # pylint: disable=unused-argument
     def git_operation(self, operation, *args, **kwargs):
-        command = self._git_operation_command(operation, args)
+        newargs = []
+        for a in args:
+            # Do not use ssh interface
+            if isinstance(a, str):
+                a = a.replace("[email protected]:", "https://github.com/")
+            newargs.append(a)
+
+        command = self._git_command(operation, *newargs)
         if isinstance(command, list):
             try:
                 status, output = utils.execute_subprocess(command, status_to_caller=True, output_to_caller=True)

.lib/git_fleximod/submodule.py

@@ -119,27 +119,25 @@ def status(self):
                                 atag = atag[:-1]
                             if atag == self.fxtag:
                                 break
-
-                
-                #print(f"line is {line} ahash is {ahash} atag is {atag} {parts}")
-                #                atag = git.git_operation("describe", "--tags", "--always")
-                # ahash =  git.git_operation("rev-list", "HEAD").partition("\n")[0]
-                    
                 recurse = False
                 if rurl != self.url:
                     remote = self._add_remote(git)
                     git.git_operation("fetch", remote)
+                # Asked for a tag and found that tag
                 if self.fxtag and atag == self.fxtag:
                     result = f"  {self.name:>20} at tag {self.fxtag}"
                     recurse = True
                     testfails = False
+                # Asked for and found a hash
                 elif self.fxtag and (ahash[: len(self.fxtag)] == self.fxtag or (self.fxtag.find(ahash)==0)):
                     result = f"  {self.name:>20} at hash {ahash}"
                     recurse = True
                     testfails = False
+                # Asked for and found a hash
                 elif atag == ahash:
                     result = f"  {self.name:>20} at hash {ahash}"
                     recurse = True
+                # Did not find requested tag or hash
                 elif self.fxtag:
                     result = f"s {self.name:>20} {atag} {ahash} is out of sync with .gitmodules {self.fxtag}"
                     testfails = True
@@ -396,13 +394,19 @@ async def update(self):
                 smgit = GitInterface(repodir, self.logger)
                 newremote = self._add_remote(smgit)
                 # Trying to distingush a tag from a hash
-                allowed = set(string.digits + 'abcdef') 
+                allowed = set(string.digits + 'abcdef')
+                status = 0
                 if not set(self.fxtag) <= allowed:
                     # This is a tag
                     tag = f"refs/tags/{self.fxtag}:refs/tags/{self.fxtag}"
-                    smgit.git_operation("fetch", newremote, tag)
-                smgit.git_operation("checkout", self.fxtag)
-
+                    status,_ = smgit.git_operation("fetch", newremote, tag)
+                if status == 0:
+                    status,_ = smgit.git_operation("checkout", self.fxtag)
+                if status:
+                    utils.fatal_error(
+                        f"Failed to checkout {self.name} at tag or hash {self.fxtag} from {repodir}"
+                    )
+                    
             if not os.path.exists(os.path.join(repodir, ".git")):
                 utils.fatal_error(
                     f"Failed to checkout {self.name} {repo_exists} {repodir} {self.path}"

.lib/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "1.0.1"
+version = "1.0.2"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <[email protected]>"]
 maintainers = ["Jim Edwards <[email protected]>"]

.lib/tbump.toml

@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "1.0.1"
+current = "1.0.2"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

.lib/tests/test_c_required.py

@@ -1,4 +1,5 @@
 import pytest
+import re
 from pathlib import Path
 
 def test_required(git_fleximod, test_repo, shared_repos):
@@ -28,3 +29,15 @@ def test_required(git_fleximod, test_repo, shared_repos):
     assert result.returncode == 0
     status = git_fleximod(test_repo, f"status {repo_name}")
     assert shared_repos["status4"] in status.stdout
+
+    text = file_path.read_text()
+    new_value = "somethingelse"
+    pattern = r"(^\s*fxtag\s*=\s*).*$"
+    replacement = r"\1" + new_value
+    new_text = re.sub(pattern, replacement, text, flags=re.MULTILINE)
+
+    # Write updated content back to file
+    file_path.write_text(new_text)
+
+    result = git_fleximod(test_repo, f"update {repo_name}")
+    assert f'fatal: couldn\'t find remote ref' in result.stderr or 'error: pathspec \'somethingelse\' did not match any file(s) known to git' in result.stderr