Merge remote-tracking branch 'origin/release' into feat/awicm3_v3.3_a…

…nd_v3.4

.github/workflows/esm_tools_actions_novm.yml

@@ -12,8 +12,13 @@ jobs:
           LC_ALL: en_US.UTF-8
           LANG: en_US.UTF-8
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: 
+            - "3.8"
+            - "3.9"
+            - "3.10"
+            - "3.11"
     name: Python ${{ matrix.python-version }} sample
     steps:
       - uses: actions/checkout@v2

configs/components/fesom/fesom-2.6.yaml

@@ -24,10 +24,10 @@ required_plugins:
 
 choose_version:
   "2.6":
-    branch: "2.6.1"
+    branch: "2.6.4"
 
   "2.6-paleodyn":
-    branch: "2.6.1"
+    branch: "2.6.4"
     wiso_code: true
     icb_code: true
     namelist_dir: "${model_dir}/config/"

runscripts/awiesm/v2.6/PI_dynveg_nomomix_withspp_nowiso_noiceberg.yaml

@@ -0,0 +1,78 @@
+general:
+    account: "paleodyn.paleodyn"
+    setup_name: "awiesm"
+    compute_time: "01:55:00"
+    initial_date: "5001-01-01"
+    final_date: "7999-12-31"
+    base_dir: "/albedo/work/projects/p_paleo_compute/stepanek/esm_tools_6_PlioMIP3_production/PlioMIP3_experiments/"
+    nmonth: 0
+    nyear: 1
+    use_venv: False
+    with_wiso: False
+    with_icb: False
+    clean_old_rundirs_except: 2
+    clean_old_rundirs_keep_every: 50
+    version: "2.6"
+    description: >
+      PI_dynveg for PlioMIP3; with dynamic vegetation, without momix, with spp, no stable water isotopes; new model version by Lars; for spinup, stream definitions not yet optimized for production
+
+computer:
+    mail_type: "FAIL"
+    mail_user: "[email protected]"
+
+awiesm:
+    model_dir: "/albedo/work/projects/p_paleo_compute/stepanek/esm_tools_6_PlioMIP3_production/esm_tools/model_codes/awiesm-2.6"
+
+echam:
+    lresume: 1
+    ini_parent_exp_id: "PI_251_wiso_c"
+    #fake_initial_date: "5001-01-01"
+    #ini_parent_date:  "$(( ${fake_initial_date} - ${echam.time_step}seconds ))"
+    ini_parent_date: "50001231"
+    ini_parent_dir: "/albedo/work/projects/p_paleo_compute/stepanek/esm_tools_6_PlioMIP3_production/initial_conditions/PI_251_wiso_c_from_Yuchen/echam/"
+    restart_rate: 1
+    restart_unit: "years"
+    nproca: 24
+    nprocb: 24 
+    nprocar: 0 
+    nprocbr: 0 
+    use_transient_forcing: False
+    namelist_dir: "/albedo/work/projects/p_paleo_compute/stepanek/esm_tools_6_PlioMIP3_production/namelists/namelist_spinup/echam/"
+
+jsbach:
+    namelist_dir: "/albedo/work/projects/p_paleo_compute/stepanek/esm_tools_6_PlioMIP3_production/namelists/namelist_spinup/jsbach/"
+    input_sources:
+        jsbach_1850: "${fesom.mesh_dir}/tarfiles${echam.resolution}/input/jsbach/jsbach_T63CORE2_11tiles_5layers_1850.nc"
+
+fesom:
+    res: "CORE2"
+    nproc: 384
+    mesh_dir: "/albedo/work/projects/p_paleo_compute/stepanek/esm_tools_6_PlioMIP3_production/meshes/mesh_core2/"
+    namelist_dir: "/albedo/work/projects/p_paleo_compute/stepanek/esm_tools_6_PlioMIP3_production/namelists/namelist_spinup/fesom/"
+    lresume: 1
+    ini_parent_exp_id: "PI_251_wiso_c"
+    ini_parent_date: "5000-12-31"
+    ini_parent_dir: "/albedo/work/projects/p_paleo_compute/stepanek/esm_tools_6_PlioMIP3_production/initial_conditions/PI_251_wiso_c_from_Yuchen/fesom/"
+    restart_rate: 1
+    restart_unit: "y"
+    restart_first: 1
+    namelist_changes:
+        namelist.io:
+            diag_list: 
+                ldiag_Ri: remove_from_namelist
+                ldiag_turbflux: remove_from_namelist
+        namelist.tra:
+            tracer_phys: 
+                use_momix: false
+        namelist.oce:
+            oce_dyn: 
+                spp: true
+        namelist.config:
+            paths:
+                ClimateDataPath: "/albedo/work/projects/p_paleo_compute/stepanek/esm_tools_6_PlioMIP3_production/hydrography_fromXiaoXu/"
+
+oasis3mct:
+    lresume: 1
+    ini_parent_exp_id: "PI_251_wiso_c"
+    ini_parent_date: "50001231"
+    ini_parent_dir: "/albedo/work/projects/p_paleo_compute/stepanek/esm_tools_6_PlioMIP3_production/initial_conditions/PI_251_wiso_c_from_Yuchen/oasis3mct/"

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 6.43.3
+current_version = 6.45.0
 commit = True
 tag = True
 

setup.py

@@ -58,7 +58,7 @@
         "[email protected]",
         "[email protected]",
     ],
-    python_requires=">=3.6, <=3.11",
+    python_requires=">=3.6, <3.12",
     classifiers=[
         "Development Status :: 3 - Alpha",
         "Intended Audience :: Science/Research",
@@ -68,6 +68,9 @@
         "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
     ],
     description="ESM Tools external infrastructure for Earth System Modelling",
     entry_points={
@@ -114,6 +117,6 @@
     test_suite="tests",
     tests_require=test_requirements,
     url="https://github.com/esm-tools/esm_tools",
-    version="6.43.3",
+    version="6.45.0",
     zip_safe=False,
 )

src/esm_archiving/__init__.py

@@ -4,7 +4,7 @@
 
 __author__ = """Paul Gierz"""
 __email__ = "[email protected]"
-__version__ = "6.43.3"
+__version__ = "6.45.0"
 
 from .esm_archiving import (archive_mistral, check_tar_lists,
                             delete_original_data, determine_datestamp_location,

src/esm_calendar/__init__.py

@@ -2,6 +2,6 @@
 
 __author__ = """Dirk Barbi"""
 __email__ = "[email protected]"
-__version__ = "6.43.3"
+__version__ = "6.45.0"
 
 from .esm_calendar import *

src/esm_cleanup/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """Dirk Barbi"""
 __email__ = "[email protected]"
-__version__ = "6.43.3"
+__version__ = "6.45.0"

src/esm_database/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """Dirk Barbi"""
 __email__ = "[email protected]"
-__version__ = "6.43.3"
+__version__ = "6.45.0"

src/esm_environment/__init__.py

@@ -2,6 +2,6 @@
 
 __author__ = """Dirk Barbi"""
 __email__ = "[email protected]"
-__version__ = "6.43.3"
+__version__ = "6.45.0"
 
 from .esm_environment import *

src/esm_master/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = """Dirk Barbi"""
 __email__ = "[email protected]"
-__version__ = "6.43.3"
+__version__ = "6.45.0"
 
 
 from . import database

src/esm_master/software_package.py

@@ -255,8 +255,8 @@ def get_command_list(self, setup_info, vcs, general):
                 if isinstance(commands, str):
                     commands = [commands]
                 if not todo == "get":
-                    commands.insert(0, "cd " + self.destination)
-                    commands.append("cd ..")
+                    commands.insert(0, "pushd " + self.destination)
+                    commands.append("popd")
             if todo == "get":
                 if self.coupling_changes:
                     commands = []

src/esm_master/task.py

@@ -435,6 +435,8 @@ def generate_task_script(self):
     def execute(self, ignore_errors=False):
         # Calculate the number of get commands for this esm_master operation
         self.num_of_get_commands()
+        # Initialize the dirstack for imitating pushd popd
+        dirstack = []
         # Loop through the commands
         for command in self.command_list:
             repo = self.get_repo_properties_from_command(command)
@@ -481,6 +483,16 @@ def execute(self, ignore_errors=False):
                     command_spl = shlex.split(command)
                     if "cd" == command_spl[0]:
                         os.chdir(command_spl[1])
+                    elif "pushd" == command_spl[0]:
+                        # Emulates pushd (MA): yes it is horrible, but I don't
+                        # have time to rewrite esm_master right now
+                        dirstack.append(os.getcwd())
+                        os.chdir(command_spl[1])
+                    elif "popd" == command_spl[0]:
+                        # Emulates popd (MA): yes it is horrible, but I don't
+                        # have time to rewrite esm_master right now
+                        target_dir = target_dir = dirstack.pop(-1)
+                        os.chdir(target_dir)
                     else:
                         subprocess.run(
                             command_spl,

src/esm_motd/__init__.py

@@ -2,6 +2,6 @@
 
 __author__ = """Dirk Barbi"""
 __email__ = "[email protected]"
-__version__ = "6.43.3"
+__version__ = "6.45.0"
 
 from .esm_motd import *

src/esm_parser/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = """Dirk Barbi"""
 __email__ = "[email protected]"
-__version__ = "6.43.3"
+__version__ = "6.45.0"
 
 
 from .dict_to_yaml import *

src/esm_parser/esm_parser.py

@@ -2333,12 +2333,14 @@ def do_math_in_entry(tree, rhs, config):
     if "${" in str(entry):
         return entry
     entry = " " + str(entry) + " "
+    date_operation = False
     while "$((" in entry:
         math, after_math = entry.split("))", 1)
         math, before_math = math[::-1].split("(($", 1)
         math = math[::-1]
         before_math = before_math[::-1]
         if DATE_MARKER in math:
+            date_operation = True
             all_dates = []
             steps = math.split(" ")
             steps = [step for step in steps if step]
@@ -2416,12 +2418,18 @@ def do_math_in_entry(tree, rhs, config):
                     math = math + "all_dates[" + str(index) + "]"
                     index += 1
         result = eval(math)
-        if isinstance(result, list):
+        if isinstance(result, list) and date_operation:
             result = result[
                 -1
             ]  # should be extended in the future - here: if list (= if diff between dates) than result in seconds
+        elif isinstance(result, list):
+            entry = ListWithProvenance(result, None)
+            entry.set_provenance(rhs.provenance)
+            return entry
+
         result = str(result)
         entry = before_math + result + after_math
+
     # TODO MA: this is a provisional dirty fix for release. Get rid of this once a more
     # general solution is worked out
     # ORIGINAL LINE: return convert(entry.strip())

src/esm_plugin_manager/__init__.py

@@ -2,6 +2,6 @@
 
 __author__ = """Dirk Barbi, Paul Gierz, Sebastian Wahl"""
 __email__ = "[email protected]"
-__version__ = "6.43.3"
+__version__ = "6.45.0"
 
 from .esm_plugin_manager import *

src/esm_profile/__init__.py

@@ -2,6 +2,6 @@
 
 __author__ = """Dirk Barbi"""
 __email__ = "[email protected]"
-__version__ = "6.43.3"
+__version__ = "6.45.0"
 
 from .esm_profile import *

src/esm_runscripts/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = """Dirk Barbi"""
 __email__ = "[email protected]"
-__version__ = "6.43.3"
+__version__ = "6.45.0"
 
 from .batch_system import *
 from .chunky_parts import *

src/esm_tests/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = """Miguel Andres-Martinez"""
 __email__ = "[email protected]"
-__version__ = "6.43.3"
+__version__ = "6.45.0"
 
 from .initialization import *
 from .read_shipped_data import *

src/esm_tests/tests.py

@@ -112,8 +112,9 @@ def comp_test(info):
     user_info = info["user"]
     this_computer = info["this_computer"]
 
-    # Set the regex format for check compilations
+    # Set the regex formats for check compilations
     cd_format = re.compile("         cd (.*)")
+    pushd_format = re.compile("         pushd (.*)")
 
     # Set the counter to 0
     c = 0
@@ -212,14 +213,17 @@ def comp_test(info):
                     folders = []
                     # Search for the folders to be created
                     for line in out.split("\n"):
+                        found_format = ""
                         if "cd" in line and "cd .." not in line:
                             found_format = cd_format.findall(line)
-                            if len(found_format) > 0:
-                                if (
-                                    ";" not in found_format[0]
-                                    and "/" not in found_format[0]
-                                ):
-                                    folders.append(found_format[0])
+                        elif "pushd" in line and "popd" not in line:
+                            found_format = pushd_format.findall(line)
+                        if len(found_format) > 0:
+                            if (
+                                ";" not in found_format[0]
+                                and "/" not in found_format[0]
+                            ):
+                                folders.append(found_format[0])
                     if len(folders) == 0:
                         logger.warning(
                             f'NOT TESTING {model}{version}: "cd" command not found'

src/esm_tools/__init__.py

@@ -23,7 +23,7 @@
 
 __author__ = """Dirk Barbi, Paul Gierz"""
 __email__ = "[email protected]"
-__version__ = "6.43.3"
+__version__ = "6.45.0"
 
 import functools
 import inspect

src/esm_utilities/__init__.py

@@ -2,6 +2,6 @@
 
 __author__ = """Paul Gierz"""
 __email__ = "[email protected]"
-__version__ = "6.43.3"
+__version__ = "6.45.0"
 
 from .utils import *