tonik 0.1.16__tar.gz → 0.1.17__tar.gz

{tonik-0.1.16 → tonik-0.1.17}/.devcontainer/devcontainer.json

@@ -1,7 +1,7 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the
 // README at: https://github.com/devcontainers/templates/tree/main/src/python
 {
-	"name": "Python 3",
+	"name": "Tonik",
 	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
 	"image": "mcr.microsoft.com/devcontainers/python:1-3.11-bullseye",
 

{tonik-0.1.16 → tonik-0.1.17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tonik
-Version: 0.1.16
+Version: 0.1.17
 Summary: Store time series data as HDF5 files and access them through an API.
 Project-URL: Homepage, https://tsc-tools.github.io/tonik
 Project-URL: Issues, https://github.com/tsc-tools/tonik/issues

tonik-0.1.17/pyproject.toml

@@ -0,0 +1,76 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.sdist]
+exclude = [
+  "/.github",
+  "/site",
+  "/docs",
+  "/sandbox.ipynb"
+]
+
+[project]
+name = "tonik"
+version = "0.1.17"
+authors = [
+  { name="Yannik Behr", email="y.behr@gns.cri.nz" },
+  { name="Christof Mueller", email="c.mueller@gns.cri.nz" }
+]
+
+description = "Store time series data as HDF5 files and access them through an API."
+readme = "README.md"
+requires-python = ">=3.9"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "h5py>=3.8",
+    "datashader>=0.14",
+    "xarray[io,accel,parallel]",
+    "pandas>=2.0",
+    "netcdf4>=1.6",
+    "h5netcdf>=1.1",
+    "python-json-logger>=2.0",
+    "uvicorn[standard]>=0.22",
+    "fastapi>=0.112",
+    "matplotlib",
+    "zarr[remote_tests]>=3.0.3; python_version >= '3.11'",
+    "zarr[remote_tests]<3; python_version < '3.11'",
+    "s3fs"
+]
+
+[project.optional-dependencies]
+dev = ["pytest",
+       "httpx",
+       "ipykernel",
+       "mkdocs",
+       "mkdocstrings[python]",
+       "mkdocs-jupyter"]
+
+[project.urls]
+Homepage = "https://tsc-tools.github.io/tonik"
+Issues = "https://github.com/tsc-tools/tonik/issues"
+
+[project.scripts]
+tonik_api = "tonik.api:main"
+test_data = "tonik.utils:main"
+grafana_annotations = "tonik.grafana_annotations:main"
+
+[tool.pytest.ini_options]
+log_cli = true
+
+[tool.hatch.envs.test]
+dependencies = [
+  "coverage[toml]",
+  "pytest",
+  "httpx"
+]
+
+[[tool.hatch.envs.test.matrix]]
+python = ["3.11", "3.9"]
+
+[tool.hatch.envs.test.scripts]
+run-pytest = "pytest tests"

{tonik-0.1.16 → tonik-0.1.17}/src/tonik/api.py

@@ -26,8 +26,9 @@ InventoryReturnType = Union[list, dict]
 
 class TonikAPI:
 
-    def __init__(self, rootdir) -> None:
+    def __init__(self, rootdir, backend='netcdf') -> None:
         self.rootdir = rootdir
+        self.backend = backend
         self.app = FastAPI()
 
         # -- allow any origin to query API
@@ -72,7 +73,7 @@ class TonikAPI:
         _et = self.preprocess_datetime(endtime)
         g = Storage(group, rootdir=self.rootdir,
                     starttime=_st, endtime=_et,
-                    create=False)
+                    create=False, backend=self.backend)
         c = g
         if subdir:
             c = g.get_substore(*subdir)
@@ -147,7 +148,8 @@ class TonikAPI:
         return freq, dates, spec
 
     async def inventory(self, group: str, subdir: SubdirType = None, tree: bool = True) -> InventoryReturnType:
-        sg = Storage(group, rootdir=self.rootdir, create=False)
+        sg = Storage(group, rootdir=self.rootdir,
+                     create=False, backend=self.backend)
         try:
             c = sg.get_substore(*subdir)
         except TypeError:
@@ -168,7 +170,8 @@ class TonikAPI:
         _st = self.preprocess_datetime(starttime)
         _et = self.preprocess_datetime(endtime)
         sg = Storage(group, rootdir=self.rootdir,
-                     starttime=_st, endtime=_et, create=False)
+                     starttime=_st, endtime=_et, create=False,
+                     backend=self.backend)
         try:
             c = sg.get_substore(*subdir)
         except TypeError:
@@ -183,10 +186,11 @@ class TonikAPI:
 def main(argv=None):
     parser = ArgumentParser()
     parser.add_argument("--rootdir", default='/tmp')
+    parser.add_argument("--backend", default='netcdf')
     parser.add_argument("-p", "--port", default=8003, type=int)
     parser.add_argument("--host", default='0.0.0.0')
     args = parser.parse_args(argv)
-    ta = TonikAPI(args.rootdir)
+    ta = TonikAPI(args.rootdir, backend=args.backend)
     uvicorn.run(ta.app, host=args.host, port=args.port)
 
 

{tonik-0.1.16 → tonik-0.1.17}/tests/conftest.py

@@ -93,6 +93,26 @@ def setup_api(setup):
     return client, g.get_substore('MDR', '00', 'BHZ')
 
 
+@pytest.fixture(scope='module')
+def setup_api_zarr(tmp_path_factory):
+    savedir = tmp_path_factory.mktemp('vumt_test_tmp_zarr', numbered=True)
+    g = Storage('volcanoes', rootdir=savedir, backend='zarr')
+    from tonik.api import TonikAPI
+    ta = TonikAPI(str(savedir), backend='zarr')
+    client = TestClient(ta.app)
+    g.starttime = datetime(2023, 1, 1)
+    g.endtime = datetime(2023, 1, 6)
+    feat = generate_test_data(tstart=tstart,
+                              feature_names=['ssam'],
+                              ndays=ndays,
+                              nfreqs=8,
+                              freq_names=['frequency'],
+                              dim=2)
+    c = g.get_substore('MDR', '00', 'BHZ')
+    c.save(feat)
+    return client, c
+
+
 @pytest.fixture(scope='module')
 def setup_multi_dimensional(tmp_path_factory):
     tempdir = tmp_path_factory.mktemp('test_xarray2zarr_high_dimensionality')

{tonik-0.1.16 → tonik-0.1.17}/tests/test_api.py

@@ -96,6 +96,36 @@ def test_read_ssam(setup_api):
     assert len(np.unique(df['freqs'])) == 8
 
 
+def test_read_ssam_from_zarr(setup_api_zarr):
+    client, l = setup_api_zarr
+    params = dict(name='ssam',
+                  group='volcanoes',
+                  subdir=['MDR', '00', 'BHZ'],
+                  starttime=str(l.starttime),
+                  endtime=str(l.endtime),
+                  resolution='full',
+                  log=False)
+    with client.stream("GET", "/feature", params=params) as r:
+        r.read()
+        txt = r.text
+    df = pd.read_csv(StringIO(txt), parse_dates=True, index_col=0)
+    np.testing.assert_array_almost_equal(df['feature'].values,
+                                         l('ssam').values.ravel(order='C'))
+
+    params = dict(name='ssam',
+                  group='volcanoes',
+                  subdir=['MDR', '00', 'BHZ'],
+                  starttime=str(l.starttime),
+                  endtime=str(l.endtime),
+                  resolution='1D')
+    with client.stream("GET", "/feature", params=params) as r:
+        r.read()
+        txt = r.text
+    df = pd.read_csv(StringIO(txt), parse_dates=True, index_col=0)
+    assert len(np.unique(df.index)) == 5
+    assert len(np.unique(df['freqs'])) == 8
+
+
 def test_read_filterbank(setup_api):
     client, l = setup_api
     params = dict(name='filterbank',