Add cylc-flow, cylc-rose, cylc-uiserver from spack develop; update setup-meta-modules extension for Python

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():
@@ -302,11 +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))
 
@@ -697,83 +695,47 @@ 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()
+            ):
+                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(
                     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(
                 module_dir, compiler_name, compiler_version, "stack-" + python_name
@@ -783,12 +745,12 @@ 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 +760,12 @@ 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):

var/spack/repos/builtin/packages/py-cylc-flow/package.py

@@ -12,8 +12,9 @@ class PyCylcFlow(PythonPackage):
     homepage = "https://cylc.org"
     pypi = "cylc-flow/cylc-flow-8.1.4.tar.gz"
 
-    maintainers("LydDeb")
+    maintainers("LydDeb", "climbfuji")
 
+    version("8.2.3", sha256="dd5bea9e4b8dad00edd9c3459a38fb778e5a073da58ad2725bc9b84ad718e073")
     version("8.2.0", sha256="cbe35e0d72d1ca36f28a4cebe9b9040a3445a74253bc94051a3c906cf179ded0")
     version("8.1.4", sha256="d1835ac18f6f24f3115c56b2bc821185484e834a86b12fd0033ff7e4dc3c1f63")
 
@@ -24,7 +25,8 @@ class PyCylcFlow(PythonPackage):
     depends_on("py-colorama@0.4:1", type=("build", "run"))
     depends_on("py-graphene@2.1:2", type=("build", "run"))
     depends_on("py-jinja2@3.0", type=("build", "run"))
-    depends_on("py-metomi-isodatetime@3.0", type=("build", "run"))
+    depends_on("py-metomi-isodatetime@3.0", type=("build", "run"), when="@:8.2.0")
+    depends_on("py-metomi-isodatetime@3:3.1", type=("build", "run"), when="@8.2.3:")
     depends_on("py-protobuf@4.21.2:4.21", type=("build", "run"))
     depends_on("py-psutil@5.6.0:", type=("build", "run"))
     depends_on("py-pyzmq@22:", type=("build", "run"), when="@8.2:")
@@ -34,3 +36,6 @@ class PyCylcFlow(PythonPackage):
     depends_on("py-rx", type=("build", "run"))
     depends_on("py-promise", type=("build", "run"))
     depends_on("py-tomli@2:", type=("build", "run"), when="^python@:3.10")
+
+    # Non-Python dependencies
+    depends_on("graphviz", type="run")

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):

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"))
-    depends_on("py-werkzeug@0.12.2", 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"))

var/spack/repos/builtin/packages/py-metomi-isodatetime/package.py

@@ -14,6 +14,11 @@ class PyMetomiIsodatetime(PythonPackage):
 
     maintainers("LydDeb")
 
+    version("3.1.0", sha256="2ec15eb9c323d5debd0678f33af99bc9a91aa0b534ee5f65f3487aed518ebf2d")
     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)

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")