fesom1 to levels

.github/workflows/CI-test.yaml

@@ -1,7 +1,7 @@
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 
 name: Run Basic Tests
 on:
   push:
     branches: ["main"]
   pull_request:
@@ -28,10 +28,22 @@
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           if ${{ matrix.python-version == '3.12' }}; then pip install --upgrade setuptools; fi
       - name: Install package
         run: |
           python -m pip install .[dev]
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      # - name: Check internet connectivity of CI runner
+      #   run: |
+      #     sudo apt-get install -y curl
+      #     curl -s  https://packagecloud.io/install/repositories/ookla/speedtest-cli/script.deb.sh | sudo bash
+      #     sudo apt-get install -y speedtest
+      #     speedtest --accept-license
       - name: Test if data will work (Meta-Test)
         run: |
           export HDF5_DEBUG=1

conftest.py

@@ -6,6 +6,7 @@
     "tests.fixtures.config_files",
     "tests.fixtures.configs",
     "tests.fixtures.environment",
+    "tests.fixtures.example_data.awicm_recom",
     "tests.fixtures.example_data.fesom_2p6_pimesh",
     "tests.fixtures.example_data.pi_uxarray",
     "tests.fixtures.fake_data.fesom_mesh",

setup.cfg

@@ -8,6 +8,6 @@ tag_prefix = 'v'
 max-line-length = 120
 [flake8]
 max-line-length = 120
-exclude = cmip6-cmor-tables/CMIP6_CVs/src
+exclude = cmip6-cmor-tables/CMIP6_CVs/src CMIP7_DReq_Software/
 [isort]
 profile = black

setup.py

@@ -30,6 +30,13 @@ def read(filename):
     long_description=read("README.rst"),
     package_dir={"": "src"},
     packages=find_packages(where="src", exclude=("tests",)),
+    # NOTE: Please keep this list sorted! In vim, you can use
+    # visual-block mode (Ctrl-V) to select the lines and then `:sort`.
+    # or use the vim-ism (starting anywhere in the list)::
+    #
+    #   vi[:sort<CR>
+    #
+    # meaning: [v]isual [i]nside square brackets, command mode, sort, enter.
     install_requires=[
         "bokeh",
         "cerberus",
@@ -47,8 +54,10 @@ def read(filename):
         "flox",
         "h5netcdf",
         "imohash",
-        "netcdf4",  # NOTE(PG): Shouldn't be a prereq for xarray?
+        "joblib",
+        "netcdf4",
         "numbagg",
+        "numpy",
         "pendulum",
         "pint-xarray",
         "prefect[dask]",

src/pymorize/cli.py

@@ -11,6 +11,8 @@
 from rich.traceback import install as rich_traceback_install
 from streamlit.web import cli as stcli
 
+from pymorize.fesom_1p4.nodes_to_levels import convert
+
 from . import _version, caching, dev_utils
 from .cmorizer import CMORizer
 from .filecache import fc
@@ -136,7 +138,11 @@ def cache(verbose, quiet, logfile, profile_mem):
     return 0
 
 
-################################################################################
+@click.group()
+def scripts():
+    return 0
+
+
 ################################################################################
 ################################################################################
 
@@ -219,6 +225,22 @@ def directory(config_file, output_dir, verbose, quiet, logfile, profile_mem):
         cmorizer.check_rules_for_output_dir(output_dir)
 
 
+################################################################################
+################################################################################
+################################################################################
+
+################################################################################
+# COMMANDS FOR scripts
+################################################################################
+
+
+@scripts.group()
+def fesom1():
+    pass
+
+
+fesom1.add_command(convert, name="nodes-to-levels")
+
 ################################################################################
 ################################################################################
 ################################################################################
@@ -270,6 +292,7 @@ def populate_cache(files: List, verbose, quiet, logfile, profile_mem):
 cli.add_command(validate)
 cli.add_command(develop)
 cli.add_command(ssh_tunnel_cli, name="ssh-tunnel")
+cli.add_command(scripts)
 
 
 def main():

src/pymorize/fesom_1p4/__init__.py

@@ -0,0 +1,3 @@
+# Move to top-level namespace:
+from .load_mesh_data import *  # noqa: F401, F403
+from .nodes_to_levels import *  # noqa: F401, F403