From 3096809aafa848ba384fd787430f4562092685bd Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Tue, 21 Nov 2023 14:04:21 -0700
Subject: [PATCH 01/21] New package py-ansimarkup

---
 .../builtin/packages/py-ansimarkup/package.py | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-ansimarkup/package.py

diff --git a/var/spack/repos/builtin/packages/py-ansimarkup/package.py b/var/spack/repos/builtin/packages/py-ansimarkup/package.py
new file mode 100644
index 00000000000000..cd02faf7c60319
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-ansimarkup/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyAnsimarkup(PythonPackage):
+    """Produce colored terminal text with an xml-like markup"""
+
+    homepage = "https://github.com/gvalkov/python-ansimarkup"
+    pypi = "ansimarkup/ansimarkup-2.1.0.tar.gz"
+
+    maintainers("climbfuji")
+
+    version("2.1.0", sha256="7b3e3d93fecc5b64d23a6e8eb96dbc8b0b576a211829d948afb397d241a8c51b")
+
+    depends_on("python@3.6:", type=("build", "run"))
+    depends_on("py-setuptools@61:", type="build")
+    depends_on("py-colorama", type=("build", "run"))

From 52b511923c5b4dc85ad3fa79fe6853022f987d35 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Tue, 21 Nov 2023 14:05:03 -0700
Subject: [PATCH 02/21] New package py-metomi-isodatetime

---
 .../packages/py-metomi-isodatetime/package.py  | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-metomi-isodatetime/package.py

diff --git a/var/spack/repos/builtin/packages/py-metomi-isodatetime/package.py b/var/spack/repos/builtin/packages/py-metomi-isodatetime/package.py
new file mode 100644
index 00000000000000..f8f407ad295aa0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-metomi-isodatetime/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyMetomiIsodatetime(PythonPackage):
+    """Python ISO 8601 date time parser and data model/manipulation utilities"""
+
+    homepage = "https://github.com/metomi/isodatetime"
+    pypi = "metomi-isodatetime/metomi-isodatetime-1!3.1.0.tar.gz"
+
+    maintainers("climbfuji")
+
+    version("3.1.0", sha256="2ec15eb9c323d5debd0678f33af99bc9a91aa0b534ee5f65f3487aed518ebf2d")
+    depends_on("py-setuptools", type="build")

From f9a635eb374798894534b9bea774424efdf7276d Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Tue, 21 Nov 2023 14:06:11 -0700
Subject: [PATCH 03/21] New package py-graphql-relay

---
 .../packages/py-graphql-relay/package.py      | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-graphql-relay/package.py

diff --git a/var/spack/repos/builtin/packages/py-graphql-relay/package.py b/var/spack/repos/builtin/packages/py-graphql-relay/package.py
new file mode 100644
index 00000000000000..f2a3b0e9c052df
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-graphql-relay/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack.package import *
+
+
+class PyGraphqlRelay(PythonPackage):
+    """A library to help construct a graphql-py server supporting react-relay"""
+
+    homepage = "https://github.com/graphql-python/graphql-relay-py"
+    pypi = "graphql-relay/graphql-relay-3.2.0.tar.gz"
+
+    maintainers("climbfuji")
+
+    version("2.0.1", sha256="870b6b5304123a38a0b215a79eace021acce5a466bf40cd39fa18cb8528afabb")
+
+    depends_on("python@3.6:3", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+    depends_on("py-six@1.12:", type=("build", "run"))
+    depends_on("py-graphql-core@2.2:3", type=("build", "run"))
+    depends_on("py-promise@2.2:3", type=("build", "run"))

From cfe703d1ca93b22800a73628d2f28c4948c2d7a8 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Tue, 21 Nov 2023 14:06:35 -0700
Subject: [PATCH 04/21] Add py-aniso8601@7.0.0

---
 var/spack/repos/builtin/packages/py-aniso8601/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-aniso8601/package.py b/var/spack/repos/builtin/packages/py-aniso8601/package.py
index f5659a200847e9..17946429114297 100644
--- a/var/spack/repos/builtin/packages/py-aniso8601/package.py
+++ b/var/spack/repos/builtin/packages/py-aniso8601/package.py
@@ -13,5 +13,6 @@ class PyAniso8601(PythonPackage):
     pypi = "aniso8601/aniso8601-9.0.1.tar.gz"
 
     version("9.0.1", sha256="72e3117667eedf66951bb2d93f4296a56b94b078a8a95905a052611fb3f1b973")
+    version("7.0.0", sha256="513d2b6637b7853806ae79ffaca6f3e8754bdd547048f5ccc1420aec4b714f1e")
 
     depends_on("py-setuptools", type="build")

From 27263653e58ceec75db5e0e02a7f6ff49ab604c1 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Tue, 21 Nov 2023 14:17:58 -0700
Subject: [PATCH 05/21] New package py-graphene

---
 .../builtin/packages/py-graphene/package.py   | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-graphene/package.py

diff --git a/var/spack/repos/builtin/packages/py-graphene/package.py b/var/spack/repos/builtin/packages/py-graphene/package.py
new file mode 100644
index 00000000000000..aa0e52d34b3fa6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-graphene/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyGraphene(PythonPackage):
+    """GraphQL framework for Python"""
+
+    homepage = "https://graphene-python.org/"
+    pypi = "graphene/graphene-2.1.9.tar.gz"
+    maintainers("climbfuji")
+
+    version("2.1.9", sha256="b9f2850e064eebfee9a3ef4a1f8aa0742848d97652173ab44c82cc8a62b9ed93")
+
+    depends_on("py-setuptools", type="build")
+    depends_on("py-graphql-core@2.1:2", type=("build", "run"))
+    depends_on("py-graphql-relay@2:2", type=("build", "run"))
+    depends_on("py-aniso8601@3:7", type=("build", "run"))
+    depends_on("py-six@1.10:1", type=("build", "run"))

From 5918da224b2d3d1cc93d8f98e309dabfe9d86568 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Tue, 21 Nov 2023 14:19:14 -0700
Subject: [PATCH 06/21] New package py-cylc-flow

---
 .../builtin/packages/py-cylc-flow/package.py  | 41 +++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-cylc-flow/package.py

diff --git a/var/spack/repos/builtin/packages/py-cylc-flow/package.py b/var/spack/repos/builtin/packages/py-cylc-flow/package.py
new file mode 100644
index 00000000000000..90ba590dfed0a6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cylc-flow/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyCylcFlow(PythonPackage):
+    """A workflow engine for cycling systems"""
+
+    homepage = "https://cylc.github.io"
+    pypi = "cylc-flow/cylc-flow-8.2.3.tar.gz"
+
+    maintainers("climbfuji")
+
+    version("8.2.3", sha256="dd5bea9e4b8dad00edd9c3459a38fb778e5a073da58ad2725bc9b84ad718e073")
+
+    # Python dependencies
+    depends_on("python@3.7:", type=("build", "run"))
+    #tomli>=2; python_version < "3.11" - is the following correct?
+    depends_on("py-tomli@2:", type="build", when="^python@:3.10")
+    depends_on("py-ansimarkup@1:", type=("build", "run"))
+    depends_on("py-async-timeout@3:", type=("build", "run"))
+    depends_on("py-colorama@0.4:0", type=("build", "run"))
+    depends_on("py-graphene@2.1:2", type=("build", "run"))
+    depends_on("py-jinja2@3", type=("build", "run"))
+    depends_on("py-metomi-isodatetime@3:3.1", type=("build", "run"))
+    depends_on("py-protobuf@4.21.2:4.21", type=("build", "run"))
+    depends_on("py-psutil@5.6:", type=("build", "run"))
+    depends_on("py-pyzmq@22:", type=("build", "run"))
+    depends_on("py-setuptools@49:", type="build")
+    conflicts("py-setuptools@67")
+    #importlib_metadata; python_version < "3.8" - is the following correct?
+    depends_on("py-importlib-metadata", type=("build", "run"), when="^python@:3.7")
+    depends_on("py-urwid@2", type=("build", "run"))
+    depends_on("py-rx", type=("build", "run"))
+    depends_on("py-promise", type=("build", "run"))
+
+    # Non-Python dependencies
+    depends_on("graphviz", type="run")

From 47f640d46ab812b37c13b5808b871f2155405e53 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Tue, 21 Nov 2023 15:00:43 -0700
Subject: [PATCH 07/21] Add py-mepo

---
 .../repos/builtin/packages/py-mepo/package.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-mepo/package.py

diff --git a/var/spack/repos/builtin/packages/py-mepo/package.py b/var/spack/repos/builtin/packages/py-mepo/package.py
new file mode 100644
index 00000000000000..ac250adf96b70a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-mepo/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyMepo(PythonPackage):
+    """Tool to manage (m)ultiple git r(epo)sitories"""
+
+    homepage = "https://github.com/GEOS-ESM/mepo"
+    url = "https://github.com/GEOS-ESM/mepo/archive/refs/tags/v1.51.1.tar.gz"
+
+    maintainers("mathomp4", "climbfuji")
+
+    version("1.51.1", sha256="543c1e7487afb2d62e5e8c8a2f69a85af1b1951f588f3dfc7471763e90847360")
+
+    depends_on("py-pyyaml@5.4:", type=("build", "run"))

From 8b893aff01fe0c784596042338353b3f447199a9 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Mon, 4 Dec 2023 17:40:41 +0100
Subject: [PATCH 08/21] py-metomi-isodatetime: fix url parsing

---
 .../repos/builtin/packages/py-metomi-isodatetime/package.py   | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/py-metomi-isodatetime/package.py b/var/spack/repos/builtin/packages/py-metomi-isodatetime/package.py
index 241bb1f46ce628..02d38147e22715 100644
--- a/var/spack/repos/builtin/packages/py-metomi-isodatetime/package.py
+++ b/var/spack/repos/builtin/packages/py-metomi-isodatetime/package.py
@@ -18,3 +18,7 @@ class PyMetomiIsodatetime(PythonPackage):
     version("3.0.0", sha256="2141e8aaa526ea7f7f1cb883e6c8ed83ffdab73269658d84d0624f63a6e1357e")
 
     depends_on("py-setuptools", type="build")
+
+    def url_for_version(self, version):
+        url = "https://files.pythonhosted.org/packages/source/m/metomi-isodatetime/metomi-isodatetime-1!{}.tar.gz"
+        return url.format(version)

From b3c81683a4fee225f1a4958acc9ff079ef1120bc Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Mon, 4 Dec 2023 20:24:15 -0700
Subject: [PATCH 09/21] Update py-werkzeug version dependency for
 py-graphene-tornado@2.6.1

---
 var/spack/repos/builtin/packages/py-graphene-tornado/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-graphene-tornado/package.py b/var/spack/repos/builtin/packages/py-graphene-tornado/package.py
index ba44045b4c6d79..74e6cf83e2a070 100644
--- a/var/spack/repos/builtin/packages/py-graphene-tornado/package.py
+++ b/var/spack/repos/builtin/packages/py-graphene-tornado/package.py
@@ -21,5 +21,5 @@ class PyGrapheneTornado(PythonPackage):
     depends_on("py-graphene@2.1:2", type=("build", "run"))
     depends_on("py-jinja2@2.10.1:", type=("build", "run"))
     depends_on("py-tornado@5.1.0:", type=("build", "run"))
-    depends_on("py-werkzeug@0.12.2", type=("build", "run"))
+    depends_on("py-werkzeug@0.15.3", type=("build", "run"))
     depends_on("py-pytest", type=("build"))

From b91f89cd20da060e5bfe031477ff8feeccea1667 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Tue, 5 Dec 2023 08:32:43 -0700
Subject: [PATCH 10/21] Add note on diverging version requirements for
 py-werkzeug in py-graphene-tornado

---
 .../repos/builtin/packages/py-graphene-tornado/package.py      | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/py-graphene-tornado/package.py b/var/spack/repos/builtin/packages/py-graphene-tornado/package.py
index 74e6cf83e2a070..d54b40676c9b1f 100644
--- a/var/spack/repos/builtin/packages/py-graphene-tornado/package.py
+++ b/var/spack/repos/builtin/packages/py-graphene-tornado/package.py
@@ -21,5 +21,8 @@ class PyGrapheneTornado(PythonPackage):
     depends_on("py-graphene@2.1:2", type=("build", "run"))
     depends_on("py-jinja2@2.10.1:", type=("build", "run"))
     depends_on("py-tornado@5.1.0:", type=("build", "run"))
+    # py-werkzeug version requirements differ between setup.py (0.12.2)
+    # and requirements.txt (0.15.3); the latter seems to be correct,
+    # see also https://github.com/spack/spack/pull/41426
     depends_on("py-werkzeug@0.15.3", type=("build", "run"))
     depends_on("py-pytest", type=("build"))

From 7853d5c3ac7c10c7141f1714a8e3d97429a1e1df Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Tue, 5 Dec 2023 11:11:29 -0700
Subject: [PATCH 11/21] Update logic in for 'spack stack setup-meta-modules
 (lib/jcsda-emc/spack-stack/stack/meta_modules.py) for finding Python

---
 .../spack-stack/stack/meta_modules.py         | 114 ++++++------------
 1 file changed, 39 insertions(+), 75 deletions(-)

diff --git a/lib/jcsda-emc/spack-stack/stack/meta_modules.py b/lib/jcsda-emc/spack-stack/stack/meta_modules.py
index f5cc260ef9b4f2..a740c0fb15085f 100755
--- a/lib/jcsda-emc/spack-stack/stack/meta_modules.py
+++ b/lib/jcsda-emc/spack-stack/stack/meta_modules.py
@@ -137,6 +137,8 @@ def get_matched_dict(root_dir, candidate_list, sub_candidate_list=None):
                 matched_dict[matched_name] = [matched_version]
             else:
                 matched_dict[matched_name].append(matched_version)
+                # Dedupe
+                matched_dict[matched_name] = list(set(matched_dict[matched_name]))
         # MPI providers or example depend on compilers
         else:
             if matched_name not in matched_dict.keys():
@@ -697,82 +699,46 @@ def setup_meta_modules():
                         f.write(module_content)
                     logging.info("  ... writing {}".format(mpi_module_file))
 
-    try:
-        del package_name
-    except:
-        pass
     # Create python modules. Need to accommodate both external
     # Python distributions and spack-built Python distributions.
-    # If there is no package config info for Python, then we are
-    # using a spack-built Python without knowing the version - not supported.
-    if not "python" in package_config.keys():
-        raise Exception(
-            """No information on Python in package config. For external
-Python distributions, specify complete specifications. For spack-built
-Python, list the correct version in the package config"""
-        )
-    else:
-        package_name = "python"
-        if "externals" in package_config[package_name].keys():
-            # Loop through all external specs and find the
-            # latest version, this is what spack is using
-            spack_python_build = False
-            python_version = None
-            for i in range(len(package_config[package_name]["externals"])):
-                (python_name, python_version_test) = get_name_and_version_from_spec(
-                    package_config[package_name]["externals"][i]["spec"]
-                )
-                if not python_version or versiontuple(python_version_test) > versiontuple(
-                    python_version
-                ):
-                    python_version = python_version_test
-                    python_package_config = package_config[python_name]["externals"][i]
-            logging.debug("  ... using external python version {}".format(python_version))
-        else:
-            spack_python_build = True
-            python_name = "python"
-            python_version = None
-            python_package_config = None
-            # Loop through versions, pick the most-recent
-            for python_version_test in package_config[package_name]["version"]:
-                if not python_version or versiontuple(python_version_test) > versiontuple(
-                    python_version
-                ):
-                    python_version = python_version_test
-            logging.debug("  ... using spack-built python version {}".format(python_version))
-            # Check that the Python version we determined is indeed what's installed
-            python_candidate_list = ["python@{}".format(python_version)]
-            for compiler_name in compiler_dict.keys():
-                for compiler_version in compiler_dict[compiler_name]:
-                    compiler_install_dir = os.path.join(
-                        install_dir, compiler_name, compiler_version
-                    )
-                    python_dict = get_matched_dict(compiler_install_dir, python_candidate_list)
-            logging.info(" ... stack python providers: '{}'".format(python_dict))
-            if not python_dict:
-                user_input = input(
-                    "No matching Python version found found, proceed without creating Python modules? (yes/no): "
-                )
-                if not user_input.lower() in ["yes", "y"]:
-                    raise Exception(
-                        """"No matching Python version found. Make sure that the
-Python version in the package config matches what spack installed."""
-                    )
-                else:
-                    logging.info(
-                        "Metamodule generation completed successfully in {}".format(
-                            meta_module_dir
-                        )
-                    )
-                    return
+    python_dict = {}
+    python_name = "python"
+
+    # First, collect all Python packages in the environment
+    for spec in ev.installed_specs():
+        if spec.name == python_name:
+            compiler_name = spec.compiler.name
+            compiler_version = str(spec.compiler.version)
+            if not compiler_name in python_dict.keys():
+                python_dict[compiler_name] = {}
+            if compiler_version in python_dict[compiler_name].keys():
+                raise Exception("Duplicate Python packages for compiler {spec.compiler}")
+            python_dict[compiler_name][compiler_version] = spec
 
     for compiler_name in compiler_dict.keys():
         for compiler_version in compiler_dict[compiler_name]:
+            if not compiler_name in python_dict.keys() or \
+                    not compiler_version in python_dict[compiler_name].keys():
+                user_input = input(
+                    f"No Python version found for compiler {compiler_name}@{compiler_version}, proceed without creating Python modules? (yes/no): "
+                    )
+                if not user_input.lower() in ["yes", "y"]:
+                    raise Exception(f"No Python version found for compiler {compiler_name}@{compiler_version}.")
+                else:
+                    continue
+            spec = python_dict[compiler_name][compiler_version]
+            python_version = str(spec.version)
             logging.info(
                 "  ... configuring stack python interpreter {}@{} for compiler {}@{}".format(
-                    python_name, python_version, compiler_name, compiler_version
+                    python_name, python_version, compiler_name, compiler_version)
                 )
-            )
+
+            if spec.external:
+                logging.debug(f"  ... using external python version {python_version}")
+                prefix = spec.external_path
+                modules = spec.external_modules
+            else:
+                logging.debug(f"  ... using spack-built python version {python_version}")
 
             # Path and name for lua module file
             python_module_dir = os.path.join(
@@ -783,12 +749,12 @@ def setup_meta_modules():
             )
 
             substitutes = SUBSTITUTES_TEMPLATE.copy()
-            #
-            if spack_python_build:
+            # Spack-built Python vs external Python
+            if not spec.external:
                 module = "python/{}".format(python_version)
                 # Load spack python module
                 substitutes["MODULELOADS"] += module_load_command(module_choice, module)
-            elif "modules" in python_package_config.keys():
+            elif modules:
                 # Existing non-spack modules to load
                 for module in python_package_config["modules"]:
                     substitutes["MODULELOADS"] += module_load_command(module_choice, module)
@@ -798,14 +764,12 @@ def setup_meta_modules():
                 logging.debug("  ... ... MODULELOADS: {}".format(substitutes["MODULELOADS"]))
                 logging.debug("  ... ... MODULEPREREQS: {}".format(substitutes["MODULEPREREQS"]))
                 # python_name_ROOT - replace "-" in python_name with "_" for environment variables
-                if "prefix" in python_package_config.keys():
-                    prefix = python_package_config["prefix"]
+                if prefix:
                     substitutes["PYTHONROOT"] = setenv_command(
                         module_choice, python_name.replace("-", "_") + "_ROOT", prefix
                     )
                     logging.debug("  ... ... PYTHONROOT: {}".format(substitutes["PYTHONROOT"]))
-            elif "prefix" in python_package_config.keys():
-                prefix = python_package_config["prefix"]
+            elif prefix:
                 # PATH
                 bindir = os.path.join(prefix, "bin")
                 if os.path.isdir(bindir):

From b32d6d59ccc3c6d3881df99174cd8aadf266b8ea Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Thu, 7 Dec 2023 08:29:28 -0700
Subject: [PATCH 12/21] Remove unnecessary and wrong package py-mepo

---
 .../repos/builtin/packages/py-mepo/package.py | 19 -------------------
 1 file changed, 19 deletions(-)
 delete mode 100644 var/spack/repos/builtin/packages/py-mepo/package.py

diff --git a/var/spack/repos/builtin/packages/py-mepo/package.py b/var/spack/repos/builtin/packages/py-mepo/package.py
deleted file mode 100644
index ac250adf96b70a..00000000000000
--- a/var/spack/repos/builtin/packages/py-mepo/package.py
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class PyMepo(PythonPackage):
-    """Tool to manage (m)ultiple git r(epo)sitories"""
-
-    homepage = "https://github.com/GEOS-ESM/mepo"
-    url = "https://github.com/GEOS-ESM/mepo/archive/refs/tags/v1.51.1.tar.gz"
-
-    maintainers("mathomp4", "climbfuji")
-
-    version("1.51.1", sha256="543c1e7487afb2d62e5e8c8a2f69a85af1b1951f588f3dfc7471763e90847360")
-
-    depends_on("py-pyyaml@5.4:", type=("build", "run"))

From 1fe069dfdbdf4f1a6cddc76b27b41df7a4719177 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Thu, 7 Dec 2023 13:36:29 -0700
Subject: [PATCH 13/21] Fix style errors in
 lib/jcsda-emc/spack-stack/stack/meta_modules.py

---
 lib/jcsda-emc/spack-stack/stack/meta_modules.py | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/lib/jcsda-emc/spack-stack/stack/meta_modules.py b/lib/jcsda-emc/spack-stack/stack/meta_modules.py
index a740c0fb15085f..f662c1f9f87d8e 100755
--- a/lib/jcsda-emc/spack-stack/stack/meta_modules.py
+++ b/lib/jcsda-emc/spack-stack/stack/meta_modules.py
@@ -717,21 +717,26 @@ def setup_meta_modules():
 
     for compiler_name in compiler_dict.keys():
         for compiler_version in compiler_dict[compiler_name]:
-            if not compiler_name in python_dict.keys() or \
-                    not compiler_version in python_dict[compiler_name].keys():
+            if (
+                not compiler_name in python_dict.keys()
+                or not compiler_version in python_dict[compiler_name].keys()
+            ):
                 user_input = input(
                     f"No Python version found for compiler {compiler_name}@{compiler_version}, proceed without creating Python modules? (yes/no): "
-                    )
+                )
                 if not user_input.lower() in ["yes", "y"]:
-                    raise Exception(f"No Python version found for compiler {compiler_name}@{compiler_version}.")
+                    raise Exception(
+                        f"No Python version found for compiler {compiler_name}@{compiler_version}."
+                    )
                 else:
                     continue
             spec = python_dict[compiler_name][compiler_version]
             python_version = str(spec.version)
             logging.info(
                 "  ... configuring stack python interpreter {}@{} for compiler {}@{}".format(
-                    python_name, python_version, compiler_name, compiler_version)
+                    python_name, python_version, compiler_name, compiler_version
                 )
+            )
 
             if spec.external:
                 logging.debug(f"  ... using external python version {python_version}")

From 6c5d71ac98eecae8d080b35694b66534e1f5e618 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Thu, 7 Dec 2023 14:10:23 -0700
Subject: [PATCH 14/21] Add variants ecflow and cylc for ewok-env

---
 .../jcsda-emc-bundles/packages/ewok-env/package.py    | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/jcsda-emc-bundles/packages/ewok-env/package.py b/var/spack/repos/jcsda-emc-bundles/packages/ewok-env/package.py
index fc0b4a54a1b5c7..f08e452a2191fa 100644
--- a/var/spack/repos/jcsda-emc-bundles/packages/ewok-env/package.py
+++ b/var/spack/repos/jcsda-emc-bundles/packages/ewok-env/package.py
@@ -17,6 +17,10 @@ class EwokEnv(BundlePackage):
 
     version("1.0.0")
 
+    # Variants for workflow engines
+    variant("ecflow", default=True, description="Use ecflow workflow engine")
+    variant("cylc", default=False, description="Use cylc workflow engine"
+
     # Variants defining repositories that are not yet publicly available
     variant("solo", default=False, description="Build solo (general tools for Python programmers)")
     variant(
@@ -41,7 +45,12 @@ class EwokEnv(BundlePackage):
     depends_on("py-ruamel-yaml-clib", type="run")
 
     # Workflow engines
-    depends_on("ecflow", type="run")
+    with when("+ecflow"):
+        depends_on("ecflow", type="run")
+    with when("+cylc"):
+        depends_on("py-cylc-flow", type="run")
+        depends_on("py-cylc-rose", type="run")
+        depends_on("py-cylc-uiserver", type="run")
 
     # R2D2 mysql backend
     depends_on("mysql", type="run")

From 6d014848da0b45a95360f0db96e44333437d3884 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Mon, 11 Dec 2023 07:42:36 -0700
Subject: [PATCH 15/21] Fix typo in
 var/spack/repos/jcsda-emc-bundles/packages/ewok-env/package.py

---
 var/spack/repos/jcsda-emc-bundles/packages/ewok-env/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/jcsda-emc-bundles/packages/ewok-env/package.py b/var/spack/repos/jcsda-emc-bundles/packages/ewok-env/package.py
index f08e452a2191fa..d0c82cbca9f742 100644
--- a/var/spack/repos/jcsda-emc-bundles/packages/ewok-env/package.py
+++ b/var/spack/repos/jcsda-emc-bundles/packages/ewok-env/package.py
@@ -19,7 +19,7 @@ class EwokEnv(BundlePackage):
 
     # Variants for workflow engines
     variant("ecflow", default=True, description="Use ecflow workflow engine")
-    variant("cylc", default=False, description="Use cylc workflow engine"
+    variant("cylc", default=False, description="Use cylc workflow engine")
 
     # Variants defining repositories that are not yet publicly available
     variant("solo", default=False, description="Build solo (general tools for Python programmers)")

From d75abcc80043d727a4249703ab04776272c0d741 Mon Sep 17 00:00:00 2001
From: Alex Richert <82525672+AlexanderRichert-NOAA@users.noreply.github.com>
Date: Mon, 11 Dec 2023 02:15:01 -0800
Subject: [PATCH 16/21] fms: add v2023.04 (#41475)

---
 var/spack/repos/builtin/packages/fms/package.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/fms/package.py b/var/spack/repos/builtin/packages/fms/package.py
index 17b7aa4322ec1c..eddab2b866b7c6 100644
--- a/var/spack/repos/builtin/packages/fms/package.py
+++ b/var/spack/repos/builtin/packages/fms/package.py
@@ -17,12 +17,7 @@ class Fms(CMakePackage):
     git = "https://github.com/NOAA-GFDL/FMS.git"
 
     maintainers("AlexanderRichert-NOAA", "Hang-Lei-NOAA", "edwardhartnett", "rem1776", "climbfuji")
-
     version("2023.04", sha256="feb895ea2b3269ca66df296199a36af335f0dc281e2dab2f1bfebb19fd9c22c4")
-    version("2023.03", sha256="008a9ff394efe6a8adbcf37dd45ca103e00ae25748fc2960b7bc54f2f3b08d85")
-    version(
-        "2023.02.01", sha256="1597f7a485d02e401ce76444b2401060d74bd032cbb060cef917f001b4ff14bc"
-    )
     version("2023.02", sha256="dc029ffadfd82c334f104268bedd8635c77976485f202f0966ae4cf06d2374be")
     version(
         "2023.01.01", sha256="f83e2814a1e3ba439ab847ec8bb251f3889d5ca14fb20849507590adbbe8e899"

From bd372d2f82b1942e5714c6c0c8c53405d047f4d0 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Mon, 11 Dec 2023 11:18:05 -0700
Subject: [PATCH 17/21] Add @climbfuji to fms maintainers (#41550)

---
 var/spack/repos/builtin/packages/fms/package.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/var/spack/repos/builtin/packages/fms/package.py b/var/spack/repos/builtin/packages/fms/package.py
index eddab2b866b7c6..17b7aa4322ec1c 100644
--- a/var/spack/repos/builtin/packages/fms/package.py
+++ b/var/spack/repos/builtin/packages/fms/package.py
@@ -17,7 +17,12 @@ class Fms(CMakePackage):
     git = "https://github.com/NOAA-GFDL/FMS.git"
 
     maintainers("AlexanderRichert-NOAA", "Hang-Lei-NOAA", "edwardhartnett", "rem1776", "climbfuji")
+
     version("2023.04", sha256="feb895ea2b3269ca66df296199a36af335f0dc281e2dab2f1bfebb19fd9c22c4")
+    version("2023.03", sha256="008a9ff394efe6a8adbcf37dd45ca103e00ae25748fc2960b7bc54f2f3b08d85")
+    version(
+        "2023.02.01", sha256="1597f7a485d02e401ce76444b2401060d74bd032cbb060cef917f001b4ff14bc"
+    )
     version("2023.02", sha256="dc029ffadfd82c334f104268bedd8635c77976485f202f0966ae4cf06d2374be")
     version(
         "2023.01.01", sha256="f83e2814a1e3ba439ab847ec8bb251f3889d5ca14fb20849507590adbbe8e899"

From 9e24e59a4eec2d0cf64c49c4c8d8a8cbe3bb3b7d Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Mon, 11 Dec 2023 16:31:52 -0700
Subject: [PATCH 18/21] Skip 'icc.patch' in
 var/spack/repos/builtin/packages/py-gevent/package.py for py-gevent@23.7.0+

---
 var/spack/repos/builtin/packages/py-gevent/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-gevent/package.py b/var/spack/repos/builtin/packages/py-gevent/package.py
index c41b815ef24320..7216c0c6d6dde2 100644
--- a/var/spack/repos/builtin/packages/py-gevent/package.py
+++ b/var/spack/repos/builtin/packages/py-gevent/package.py
@@ -39,7 +39,7 @@ class PyGevent(PythonPackage):
     conflicts("^py-cython@3:", when="@:20.5.0")
 
     # Deprecated compiler options. upstream PR: https://github.com/gevent/gevent/pull/1896
-    patch("icc.patch", when="%intel")
+    patch("icc.patch", when="@:21.12.0 %intel")
 
     @run_before("install")
     def recythonize(self):

From b0baa0ad356a7168fd74cf9020375079e56179d6 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Mon, 11 Dec 2023 19:43:14 -0700
Subject: [PATCH 19/21] Proceed without MPI or Python modules if not in
 environment

---
 lib/jcsda-emc/spack-stack/stack/meta_modules.py | 17 +++--------------
 1 file changed, 3 insertions(+), 14 deletions(-)

diff --git a/lib/jcsda-emc/spack-stack/stack/meta_modules.py b/lib/jcsda-emc/spack-stack/stack/meta_modules.py
index f662c1f9f87d8e..b6e18f30cb198a 100755
--- a/lib/jcsda-emc/spack-stack/stack/meta_modules.py
+++ b/lib/jcsda-emc/spack-stack/stack/meta_modules.py
@@ -304,11 +304,7 @@ def setup_meta_modules():
     # Then, check for mpi providers - recursively for compilers
     mpi_dict = get_matched_dict(module_dir, mpi_candidate_list, compiler_candidate_list)
     if not mpi_dict:
-        user_input = input(
-            "No matching MPI providers found, proceed without creating MPI module hierarchy? (yes/no): "
-        )
-        if not user_input.lower() in ["yes", "y"]:
-            raise Exception("No matching MPI providers found")
+        logging.warn("No matching MPI providers found, skipping MPI module hierarchy")
     else:
         logging.info(" ... stack mpi providers: '{}'".format(mpi_dict))
 
@@ -721,15 +717,8 @@ def setup_meta_modules():
                 not compiler_name in python_dict.keys()
                 or not compiler_version in python_dict[compiler_name].keys()
             ):
-                user_input = input(
-                    f"No Python version found for compiler {compiler_name}@{compiler_version}, proceed without creating Python modules? (yes/no): "
-                )
-                if not user_input.lower() in ["yes", "y"]:
-                    raise Exception(
-                        f"No Python version found for compiler {compiler_name}@{compiler_version}."
-                    )
-                else:
-                    continue
+                logging.warn("No Python version found for compiler {compiler_name}@{compiler_version}, skipping Python modules")
+                continue
             spec = python_dict[compiler_name][compiler_version]
             python_version = str(spec.version)
             logging.info(

From e256fe22ad1aa0a4ec49b0b82669f23e8e07f31e Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Mon, 11 Dec 2023 20:48:09 -0700
Subject: [PATCH 20/21] Fix formatting errors in
 lib/jcsda-emc/spack-stack/stack/meta_modules.py

---
 black.patch                                     | 17 +++++++++++++++++
 lib/jcsda-emc/spack-stack/stack/meta_modules.py |  4 +++-
 2 files changed, 20 insertions(+), 1 deletion(-)
 create mode 100644 black.patch

diff --git a/black.patch b/black.patch
new file mode 100644
index 00000000000000..41b8bdfe5a6c59
--- /dev/null
+++ b/black.patch
@@ -0,0 +1,17 @@
+--- lib/jcsda-emc/spack-stack/stack/meta_modules.py	2023-12-12 02:44:14.068945+00:00
++++ lib/jcsda-emc/spack-stack/stack/meta_modules.py	2023-12-12 02:44:27.720853+00:00
+@@ -715,11 +715,13 @@
+         for compiler_version in compiler_dict[compiler_name]:
+             if (
+                 not compiler_name in python_dict.keys()
+                 or not compiler_version in python_dict[compiler_name].keys()
+             ):
+-                logging.warn("No Python version found for compiler {compiler_name}@{compiler_version}, skipping Python modules")
++                logging.warn(
++                    "No Python version found for compiler {compiler_name}@{compiler_version}, skipping Python modules"
++                )
+                 continue
+             spec = python_dict[compiler_name][compiler_version]
+             python_version = str(spec.version)
+             logging.info(
+                 "  ... configuring stack python interpreter {}@{} for compiler {}@{}".format(
diff --git a/lib/jcsda-emc/spack-stack/stack/meta_modules.py b/lib/jcsda-emc/spack-stack/stack/meta_modules.py
index b6e18f30cb198a..6a8061e8193588 100755
--- a/lib/jcsda-emc/spack-stack/stack/meta_modules.py
+++ b/lib/jcsda-emc/spack-stack/stack/meta_modules.py
@@ -717,7 +717,9 @@ def setup_meta_modules():
                 not compiler_name in python_dict.keys()
                 or not compiler_version in python_dict[compiler_name].keys()
             ):
-                logging.warn("No Python version found for compiler {compiler_name}@{compiler_version}, skipping Python modules")
+                logging.warn(
+                    "No Python version found for compiler {compiler_name}@{compiler_version}, skipping Python modules"
+                )
                 continue
             spec = python_dict[compiler_name][compiler_version]
             python_version = str(spec.version)

From aa011fc3279dee2e89266d148798bb871f4c1d7f Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Tue, 12 Dec 2023 09:21:22 -0700
Subject: [PATCH 21/21] Remove black.patch

---
 black.patch | 17 -----------------
 1 file changed, 17 deletions(-)
 delete mode 100644 black.patch

diff --git a/black.patch b/black.patch
deleted file mode 100644
index 41b8bdfe5a6c59..00000000000000
--- a/black.patch
+++ /dev/null
@@ -1,17 +0,0 @@
---- lib/jcsda-emc/spack-stack/stack/meta_modules.py	2023-12-12 02:44:14.068945+00:00
-+++ lib/jcsda-emc/spack-stack/stack/meta_modules.py	2023-12-12 02:44:27.720853+00:00
-@@ -715,11 +715,13 @@
-         for compiler_version in compiler_dict[compiler_name]:
-             if (
-                 not compiler_name in python_dict.keys()
-                 or not compiler_version in python_dict[compiler_name].keys()
-             ):
--                logging.warn("No Python version found for compiler {compiler_name}@{compiler_version}, skipping Python modules")
-+                logging.warn(
-+                    "No Python version found for compiler {compiler_name}@{compiler_version}, skipping Python modules"
-+                )
-                 continue
-             spec = python_dict[compiler_name][compiler_version]
-             python_version = str(spec.version)
-             logging.info(
-                 "  ... configuring stack python interpreter {}@{} for compiler {}@{}".format(