Merge pull request #30 from ecmwf/develop

Small changes in GitHub Actions and version

.github/workflows/hpc-module.yml

@@ -0,0 +1,54 @@
+name: hpc-module
+
+on:
+  workflow_dispatch:
+      inputs:
+        module-name: 
+          description: 'Module name'
+          required: true
+          type: string
+        module-tag:
+          description: 'Module tag'
+          required: false
+          default: 'NOT_DEFINED'
+          type: string
+  push:
+    tags:
+    - '[0-9]+.[0-9]+.[0-9]+'
+jobs:
+  install_module:
+    runs-on: [hpc]
+    steps:
+      - uses: ecmwf-actions/reusable-workflows/ci-hpc-generic@v2
+        with:
+          troika_user: ${{ secrets.HPC_CI_SSH_USER }}
+          template: |
+
+            MODULE_VERSION=${{ github.event_name == 'workflow_dispatch' && inputs.module-name || github.ref_name }}
+            MODULE_TAG=${{ github.event_name == 'workflow_dispatch' && inputs.module-tag || 'default'}}
+            HAT_BRANCH=${{ github.ref_name }}
+
+            PREFIX=/usr/local/apps/hat/${MODULE_VERSION}
+            rm -rf $PREFIX
+            mkdir -p $PREFIX
+
+            # Load the default python module
+            module load python3
+
+            PYTHONUSERBASE=$PREFIX pip3 install --user git+https://github.com/ecmwf/hat.git@${HAT_BRANCH}
+
+            module unload python3
+
+            software-sync -s local -p hat
+            module load modulemgr
+            modulemgr -f -m all sync hat
+
+            if [ $MODULE_TAG != 'NOT_DEFINED' ]
+            then
+                modulemgr -f -m all tag -o hat $MODULE_VERSION $MODULE_TAG
+            fi
+
+          sbatch_options: |
+            #SBATCH --job-name=cd_hat
+            #SBATCH --time=00:10:00
+            #SBATCH --qos=deploy

.github/workflows/on-push.yml

@@ -5,7 +5,7 @@ on:
     branches:
     - main
     tags:
-    - "*"
+    - "[0-9]+.[0-9]+.[0-9]+"
   pull_request:
     branches:
     - main

.gitignore

@@ -1,6 +1,6 @@
 
 
-# Added by Sam Murphy
+# project specific
 .DS_Store
 *.png
 *.nc
@@ -11,7 +11,7 @@
 notebooks/untracked/*
 **/data/
 .vscode/launch.json
-
+hat/_version.py
 
 # GENERIC PYTHON GITIGNORE FROM GIT HUB
 #

environment.yml

@@ -14,7 +14,6 @@ dependencies:
   - tqdm
   - typer
   - humanize
-  - typer
   - ipyleaflet
   - ipywidgets
   - pip

hat/__init__.py

@@ -3,3 +3,11 @@
 # from hat.config import read_config
 # from hat.extract_simulations import extract_simulations
 # from hat.read_observations import read_observations
+
+try:
+    # NOTE: the `_version.py` file must not be present in the git repository
+    #   as it is generated by setuptools at install time
+    from ._version import __version__
+except ImportError:  # pragma: no cover
+    # Local copy or not installed with setuptools
+    __version__ = ""

hat/extract_simulation_timeseries.py

@@ -36,7 +36,11 @@ def extract_timeseries(
 
     # all timeseries (i.e. handle proximal and duplicate stations)
     da_stations = assign_stations(
-        stations, station_mask, da_points, coords, config["station_id_column_name"]
+        stations,
+        station_mask,
+        da_points,
+        coords,
+        config["station_id_column_name"],
     )
 
     return da_stations

hat/filters.py

@@ -4,7 +4,10 @@
 
 # @st.cache_data
 def temporal_filter(
-    _metadata, _observations: pd.DataFrame, timeperiod, station_id_name="station_id"
+    _metadata,
+    _observations: pd.DataFrame,
+    timeperiod,
+    station_id_name="station_id",
 ):
     """
     filter station metadata and timeseries by timeperiod

hat/interactive/explorers.py

@@ -260,7 +260,11 @@ def __init__(self, config):
         self.title_label = ipywidgets.Label(
             "Interactive Map Visualisation for Hydrological Model Performance",
             layout=ipywidgets.Layout(justify_content="center"),
-            style={"font_weight": "bold", "font_size": "24px", "font_family": "Arial"},
+            style={
+                "font_weight": "bold",
+                "font_size": "24px",
+                "font_family": "Arial",
+            },
         )
 
         # Create the interactive widgets
@@ -302,7 +306,10 @@ def create_frame(self):
             width="40%",
         )
         right_layout = ipywidgets.Layout(
-            justify_content="center", align_items="center", spacing="2px", width="60%"
+            justify_content="center",
+            align_items="center",
+            spacing="2px",
+            width="60%",
         )
 
         # Frames

hat/interactive/leaflet.py

@@ -39,7 +39,8 @@ def __init__(
         basemap=ipyleaflet.basemaps.OpenStreetMap.Mapnik,
     ):
         self.map = ipyleaflet.Map(
-            basemap=basemap, layout=ipywidgets.Layout(width="100%", height="600px")
+            basemap=basemap,
+            layout=ipywidgets.Layout(width="100%", height="600px"),
         )
         self.legend_widget = ipywidgets.Output()
 
@@ -56,7 +57,10 @@ def _set_boundaries(self, stations_metadata, coord_names):
         min_lat, max_lat = min(lats), max(lats)
         min_lon, max_lon = min(lons), max(lons)
 
-        bounds = [(float(min_lat), float(min_lon)), (float(max_lat), float(max_lon))]
+        bounds = [
+            (float(min_lat), float(min_lon)),
+            (float(max_lat), float(max_lon)),
+        ]
         self.map.fit_bounds(bounds)
 
     def add_geolayer(self, geodata, colormap, widgets, coord_names=None):

hat/interactive/widgets.py

@@ -192,7 +192,11 @@ def __init__(self, datasets):
                 height=350,
                 margin=dict(l=120),
                 legend=dict(
-                    orientation="h", yanchor="bottom", y=1.02, xanchor="right", x=1
+                    orientation="h",
+                    yanchor="bottom",
+                    y=1.02,
+                    xanchor="right",
+                    x=1,
                 ),
                 xaxis_title="Date",
                 xaxis_tickformat="%d-%m-%Y",
@@ -262,9 +266,7 @@ def _update_title(self, metadata):
         """
         station_id = metadata["station_id"]
         station_name = metadata["StationName"]
-        updated_title = (
-            f"<b>Selected station:<br>ID: {station_id}, name: {station_name}</b> "
-        )
+        updated_title = f"<b>Selected station:<br>ID: {station_id}, name: {station_name}</b> "  # noqa: E501
         self.figure.update_layout(
             title={
                 "text": updated_title,

hat/mapping/station_mapping.py

@@ -387,7 +387,8 @@ def save_geo_dataframes(df, out_dir, cell_size):
 
     # Create GeoDataFrames
     gdf_station_point = gpd.GeoDataFrame(
-        df, geometry=[Point(xy) for xy in zip(df["station_lon"], df["station_lat"])]
+        df,
+        geometry=[Point(xy) for xy in zip(df["station_lon"], df["station_lat"])],
     )
     gdf_near_grid_polygon = gpd.GeoDataFrame(
         df, geometry=df["near_grid_polygon_wkt"].apply(loads)
@@ -408,7 +409,8 @@ def save_geo_dataframes(df, out_dir, cell_size):
         os.path.join(out_dir, "optimum_grid.geojson"), driver="GeoJSON"
     )
     gdf_line_optimum.to_file(
-        os.path.join(out_dir, "stations2grid_optimum_line.geojson"), driver="GeoJSON"
+        os.path.join(out_dir, "stations2grid_optimum_line.geojson"),
+        driver="GeoJSON",
     )
     gdf_station_point.to_csv(os.path.join(out_dir, "stations.csv"))
 

pyproject.toml

@@ -1,3 +1,101 @@
-# required for isort and black to play nicely
+
+[build-system]
+requires = ["setuptools>=65", "setuptools_scm[toml]>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "hydro_analysis_toolkit"
+requires-python = ">=3.8"
+authors = [
+    {name = "European Centre for Medium-Range Weather Forecasts (ECMWF)", email = "software.support@ecmwf.int"},
+]
+maintainers = [
+    {name = "Corentin Carton de Wiart", email = "corentin.carton@ecmwf.int"},
+]
+description = "ECMWF Hydrological Analysis Tools"
+license = {file = "LICENSE"}
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.10",
+    "Topic :: Scientific/Engineering",
+]
+dynamic = ["version", "readme"]
+
+dependencies = [
+    "numpy",
+    "pandas",
+    "xarray",
+    "matplotlib",
+    "geopandas",
+    "typer",
+    "humanize",
+    "tqdm",
+    "ipyleaflet",
+    "ipywidgets",
+    "earthkit-data",
+    "cfgrib"
+]
+
+[project.urls]
+    repository = "https://github.com/ecmwf/hat"
+    documentation = "https://hydro-analysis-toolkit.readthedocs.io"
+    issues = "https://github.com/ecmwf/hat/issues"
+
+[project.optional-dependencies]
+    test = [
+        "pytest",
+    ]
+    docs = [
+        "mkdocs",
+        "mkdocs-material",
+        "mkdocstrings-python",
+        "mkdocs-autorefs",
+        "mkdocs-gen-files",
+        "pymdown-extensions",
+        "markdown-exec[ansi]",
+    ]
+
+[project.scripts]
+    hat-extract-timeseries = "hat.tools.extract_simulation_timeseries_cli:main"
+    hat-hydrostats = "hat.tools.hydrostats_cli:main"
+    hat-stations-mapping = "hat.mapping.station_mapping:main"
+
 [tool.isort]
-profile = "black"
+profile="black"
+
+# Testing
+[tool.pytest]
+addopts = "--pdbcls=IPython.terminal.debugger:Pdb"
+testpaths = [
+    "tests",
+]
+
+# Packaging/setuptools options
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.dynamic]
+readme = {file = ["README.md"], content-type = "text/markdown"}
+
+# [tool.setuptools.package_data]
+# hat = ["config_json/*.json"]
+
+[tool.setuptools.packages.find]
+where = ["."]
+exclude = ["tests"]
+
+[tool.setuptools_scm]
+write_to = "hat/_version.py"
+write_to_template = '''
+# Do not change! Do not track in version control!
+__version__ = "{version}"
+'''
+parentdir_prefix_version='hat-'  # get version from GitHub-like tarballs
+fallback_version='0.7.1'

tests/test_interactive.py

@@ -92,7 +92,11 @@ def test_update(self):
 class TestMetaDataWidget:
     def test_update(self):
         df = pd.DataFrame(
-            {"col1": [1, 2, 3], "col2": ["a", "b", "c"], "col3": [0.1, 0.2, 0.3]}
+            {
+                "col1": [1, 2, 3],
+                "col2": ["a", "b", "c"],
+                "col3": [0.1, 0.2, 0.3],
+            }
         )
         widget = wd.MetaDataWidget(df, "col2")
         assert widget.update("a") is True

tests/test_mapping.py

@@ -74,7 +74,12 @@ def test_create_grid_polygon():
     lat, lon = 2.5, 2.5
     cell_size = 1
     polygon = create_grid_polygon(lat, lon, cell_size)
-    assert polygon.bounds == (2, 2, 3, 3)  # Check if the polygon bounds are as expected
+    assert polygon.bounds == (
+        2,
+        2,
+        3,
+        3,
+    )  # Check if the polygon bounds are as expected
 
 
 @pytest.fixture