Merge pull request #356 from euroargodev/bgc-2024

Work on BGC from 2024 LOV visit
euroargodev · Sep 25, 2024 · 549d8c3 · 549d8c3
2 parents 1e79ec0 + 2d4785d
commit 549d8c3
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diff --git a/.github/workflows/pytests-upstream.yml b/.github/workflows/pytests-upstream.yml
@@ -70,7 +70,7 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
-    timeout-minutes: 45
+#    timeout-minutes: 45
     strategy:
       fail-fast: true
       matrix:
@@ -196,7 +196,7 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
-    timeout-minutes: 45
+#    timeout-minutes: 45
     strategy:
       fail-fast: true
       matrix:

diff --git a/.github/workflows/pytests.yml b/.github/workflows/pytests.yml
@@ -47,7 +47,7 @@ jobs:
       run:
         shell: bash -l {0}
     continue-on-error: ${{ matrix.experimental }}
-    timeout-minutes: 45
+#    timeout-minutes: 45
     strategy:
       max-parallel: 12
       fail-fast: false
@@ -169,7 +169,7 @@ jobs:
       run:
         shell: bash -l {0}
     continue-on-error: ${{ matrix.experimental }}
-    timeout-minutes: 45
+#    timeout-minutes: 45
     strategy:
       max-parallel: 12
       fail-fast: false

diff --git a/argopy/__init__.py b/argopy/__init__.py
@@ -42,6 +42,7 @@
 from .utils import MonitoredThreadPoolExecutor  # noqa: E402, F401
 from .utils import monitor_status as status  # noqa: E402
 from .related import TopoFetcher, OceanOPSDeployments, ArgoNVSReferenceTables, ArgoDocs, ArgoDOI  # noqa: E402
+from .extensions import CanyonMED
 
 
 #
@@ -77,6 +78,10 @@
     "ArgoColors",  # Class
     "stores",
     "tutorial",
+
+    # Argo xarray accessor extensions
+    "CanyonMED",
+
     # Constants
     "__version__"
 )
diff --git a/argopy/data_fetchers/argovis_data.py b/argopy/data_fetchers/argovis_data.py
@@ -82,6 +82,7 @@ def __init__(
         """
         self.definition = "Argovis Argo data fetcher"
         self.dataset_id = OPTIONS["dataset"] if ds == "" else ds
+        self.user_mode = kwargs["mode"] if "mode" in kwargs else OPTIONS["mode"]
         self.server = kwargs["server"] if "server" in kwargs else api_server
         timeout = OPTIONS["api_timeout"] if api_timeout == 0 else api_timeout
         self.store_opts = {
@@ -379,14 +380,20 @@ def to_xarray(self, errors: str = "ignore"):
         ds = ds[np.sort(ds.data_vars)]
         return ds
 
+    def transform_data_mode(self, ds: xr.Dataset, **kwargs):
+        # Argovis data are already curated !
+        if ds.argo._type == "point":
+            ds["N_POINTS"] = np.arange(0, len(ds["N_POINTS"]))
+        return ds
+
     def filter_data_mode(self, ds: xr.Dataset, **kwargs):
-        # Argovis data already curated !
+        # Argovis data are already curated !
         if ds.argo._type == "point":
             ds["N_POINTS"] = np.arange(0, len(ds["N_POINTS"]))
         return ds
 
     def filter_qc(self, ds: xr.Dataset, **kwargs):
-        # Argovis data already curated !
+        # Argovis data are already curated !
         if ds.argo._type == "point":
             ds["N_POINTS"] = np.arange(0, len(ds["N_POINTS"]))
         return ds
@@ -396,7 +403,7 @@ def filter_researchmode(self, ds: xr.Dataset, *args, **kwargs) -> xr.Dataset:
 
         This filter will select only QC=1 delayed mode data with pressure errors smaller than 20db
 
-        Use this filter instead of filter_data_mode and filter_qc
+        Use this filter instead of transform_data_mode and filter_qc
         """
         ds = ds.argo.filter_researchmode()
         if ds.argo._type == "point":
@@ -521,7 +528,12 @@ def uri(self):
                 )
                 boxes = self.Chunker.fit_transform()
                 for box in boxes:
-                    urls.append(Fetch_box(box=box, ds=self.dataset_id).get_url())
+                    opts = {
+                        "ds": self.dataset_id,
+                        "fs": self.fs,
+                        "server": self.server,
+                    }
+                    urls.append(Fetch_box(box=box, **opts).get_url())
             else:
                 urls.append(self.get_url())
         else:
@@ -549,6 +561,16 @@ def uri(self):
             )
             boxes = self.Chunker.fit_transform()
             for box in boxes:
-                urls.append(Fetch_box(box=box, ds=self.dataset_id).get_url())
+                opts = {
+                    "ds": self.dataset_id,
+                    "fs": self.fs,
+                    "server": self.server,
+                }
+                urls.append(
+                    Fetch_box(
+                        box=box,
+                        **opts,
+                    ).get_url()
+                )
 
         return self.url_encode(urls)