Merge pull request #394 from euroargodev/releasev0.1.17

Prepare for v0.1.17 Bat Release 🦇

argopy/data_fetchers/erddap_data.py

@@ -620,7 +620,6 @@ def getNfromncHeader(url):
             N += getNfromncHeader(url)
         return N
 
-
     def post_process(
         self, this_ds, add_dm: bool = True, URI: list = None
     ):  # noqa: C901

argopy/data_fetchers/erddap_refdata.py

@@ -110,7 +110,6 @@ def _add_attributes(self, this):  # noqa: C901
 
         return this
 
-
     @property
     def _minimal_vlist(self):
         """Return the minimal list of variables to retrieve measurements for"""

argopy/errors.py

@@ -194,4 +194,3 @@ def __init__(self, reason: str = None, version: str = None, ignore_caller: List
 
         else:
             raise TypeError(repr(type(reason)))
-

argopy/fetchers.py

@@ -16,16 +16,16 @@
 import logging
 
 from .options import OPTIONS, _VALIDATORS
-from .errors import InvalidFetcherAccessPoint, InvalidFetcher, OptionValueError, OptionDeprecatedWarning
+from .errors import (
+    InvalidFetcherAccessPoint,
+    InvalidFetcher,
+    OptionValueError,
+    OptionDeprecatedWarning,
+)
 from .related import (
     get_coriolis_profile_id,
 )
-from .utils.checkers import (
-    is_box,
-    is_indexbox,
-    check_wmo,
-    check_cyc
-)
+from .utils.checkers import is_box, is_indexbox, check_wmo, check_cyc
 from .utils.lists import (
     list_available_data_src,
     list_available_index_src,
@@ -166,12 +166,15 @@ def __init__(self, mode: str = "", src: str = "", ds: str = "", **fetcher_kwargs
         if self._src == "argovis" and (
             self._mode == "expert" or self._mode == "research"
         ):
-            raise OptionValueError("The 'argovis' data source fetching is only available in 'standard' user mode")
+            raise OptionValueError(
+                "The 'argovis' data source fetching is only available in 'standard' user mode"
+            )
 
         if self._src == "gdac" and "ftp" in self.fetcher_kwargs:
-            OptionDeprecatedWarning(reason="The GDAC 'ftp' argument is deprecated, it will be replaced by 'gdac' in versions >= 0.1.18",
-                                   version="v0.0.17")
-
+            OptionDeprecatedWarning(
+                reason="The GDAC 'ftp' argument is deprecated, it will be replaced by 'gdac' in versions >= 0.1.18",
+                version="v0.0.17",
+            )
 
     def __repr__(self):
         para = (
@@ -306,7 +309,7 @@ def domain(self):
 
     @property
     def mission(self):
-        if self._dataset_id == 'bgc':
+        if self._dataset_id == "bgc":
             return "BGC"
         else:
             return "core+deep"
@@ -530,18 +533,21 @@ def to_index(self, full: bool = False, coriolis_id: bool = False):
         :class:`pandas.DataFrame`
             Argo-like index of fetched data
         """
+
         def prt(txt):
             msg = [txt]
             if self._request != self.__repr__():
                 msg.append(self._request)
             log.debug("\n".join(msg))
 
         def add_coriolis(this_df):
-            if 'id' not in this_df:
+            if "id" not in this_df:
                 this_df["id"] = None
 
                 def fc(row):
-                    row["id"] = get_coriolis_profile_id(row["wmo"], row["cyc"])["ID"].values[0]
+                    row["id"] = get_coriolis_profile_id(row["wmo"], row["cyc"])[
+                        "ID"
+                    ].values[0]
                     return row
 
                 this_df = this_df.apply(fc, axis=1)
@@ -550,7 +556,9 @@ def fc(row):
         # With the gdac and erddap+bgc,
         # we rely on the fetcher ArgoIndex:
         # (hence we always return a full index)
-        if (self._src == 'erddap' and self._dataset_id == 'bgc') or (self._src == 'gdac'):
+        if (self._src == "erddap" and self._dataset_id == "bgc") or (
+            self._src == "gdac"
+        ):
             prt("to_index working with fetcher ArgoIndex instance")
             idx = self.fetcher.indexfs
             if self._AccessPoint == "region":
@@ -564,7 +572,9 @@ def fc(row):
             if self._AccessPoint == "float":
                 idx.search_wmo(self._AccessPoint_data["wmo"])
             if self._AccessPoint == "profile":
-                idx.search_wmo_cyc(self._AccessPoint_data["wmo"], self._AccessPoint_data["cyc"])
+                idx.search_wmo_cyc(
+                    self._AccessPoint_data["wmo"], self._AccessPoint_data["cyc"]
+                )
 
             # Then export search result to Index dataframe:
             df = idx.to_dataframe()
@@ -611,14 +621,14 @@ def fc(row):
                 df = add_coriolis(df) if coriolis_id else df
 
                 # Possibly replace the light index with the full version:
-                if 'profiler_code' not in df or self._request == self.__repr__():
+                if "profiler_code" not in df or self._request == self.__repr__():
                     prt("to_index replaced the light index with the full version")
                     self._index = df
 
         return df
 
     def load(self, force: bool = False, **kwargs):
-        """ Fetch data (and compute a profile index) if not already in memory
+        """Fetch data (and compute a profile index) if not already in memory
 
         Apply the default to_xarray() and to_index() methods and store results in memory.
         You can access loaded measurements structure with the `data` and `index` properties.
@@ -752,11 +762,6 @@ def __init__(
         _VALIDATORS["src"](self._src)
 
         # Load data source access points:
-        if self._src == "localftp":
-            raise ValueError(
-                "The 'localftp' data source is deprecated. It's been replaced by 'gdac'."
-            )
-
         if self._src not in AVAILABLE_INDEX_SOURCES:
             raise InvalidFetcher(
                 "Requested index fetcher '%s' not available ! "

argopy/options.py

@@ -4,22 +4,28 @@
 # Like always, largely inspired by xarray code:
 # https://github.com/pydata/xarray/blob/cafab46aac8f7a073a32ec5aa47e213a9810ed54/xarray/core/options.py
 """
+
 import os
 import warnings
 import logging
 import fsspec
 from fsspec.core import split_protocol
 from socket import gaierror
 from urllib.parse import urlparse
-from .errors import OptionValueError, FtpPathError, ErddapPathError, OptionDeprecatedWarning
+from .errors import (
+    OptionValueError,
+    FtpPathError,
+    ErddapPathError,
+    OptionDeprecatedWarning,
+)
 
 # Define a logger
 log = logging.getLogger("argopy.options")
 
 # Define option names as seen by users:
 DATA_SOURCE = "src"
 FTP = "ftp"
-ERDDAP = 'erddap'
+ERDDAP = "erddap"
 DATASET = "dataset"
 CACHE_FOLDER = "cachedir"
 CACHE_EXPIRATION = "cache_expiration"
@@ -62,15 +68,15 @@ def _positive_integer(value):
 
 def validate_ftp(this_path):
     if this_path != "-":
-        return check_gdac_path(this_path, errors='raise')
+        return check_gdac_path(this_path, errors="raise")
     else:
         log.debug("OPTIONS['%s'] is not defined" % FTP)
         return False
 
 
 def validate_http(this_path):
     if this_path != "-":
-        return check_erddap_path(this_path, errors='raise')
+        return check_erddap_path(this_path, errors="raise")
     else:
         log.debug("OPTIONS['%s'] is not defined" % ERDDAP)
         return False
@@ -186,16 +192,20 @@ def __init__(self, **kwargs):
                 raise OptionValueError(f"option {k!r} given an invalid value: {v!r}")
             self.old[k] = OPTIONS[k]
 
-            if k == 'dataset':
-                OptionDeprecatedWarning(reason="The 'dataset' option is deprecated, it will be replaced by 'ds' in "
-                                            "versions >= 0.1.18",
-                                     version="v0.0.17",
-                                     ignore_caller='test_opt_dataset')
+            if k == "dataset":
+                OptionDeprecatedWarning(
+                    reason="The 'dataset' option is deprecated, it will be replaced by 'ds' in "
+                    "versions >= 0.1.18",
+                    version="v0.0.17",
+                    ignore_caller="test_opt_dataset",
+                )
 
-            if k == 'ftp':
-                OptionDeprecatedWarning(reason="The 'ftp' option is deprecated, it will be replaced by 'gdac' in "
-                                            "versions >= 0.1.18",
-                                     version="v0.0.17")
+            if k == "ftp":
+                OptionDeprecatedWarning(
+                    reason="The 'ftp' option is deprecated, it will be replaced by 'gdac' in "
+                    "versions >= 0.1.18",
+                    version="v0.0.17",
+                )
 
         self._apply_update(kwargs)
 
@@ -214,9 +224,9 @@ def reset_options():
     set_options(**DEFAULT)
 
 
-def check_erddap_path(path, errors='ignore'):
+def check_erddap_path(path, errors="ignore"):
     """Check if an url points to an ERDDAP server"""
-    fs = fsspec.filesystem('http', ssl=False)
+    fs = fsspec.filesystem("http", ssl=False)
     check1 = fs.exists(path + "/info/index.json")
     if check1:
         return True
@@ -230,60 +240,62 @@ def check_erddap_path(path, errors='ignore'):
         return False
 
 
-def check_gdac_path(path, errors='ignore'):  # noqa: C901
-    """ Check if a path has the expected GDAC ftp structure
-
-        Check if a path is structured like:
-        .
-        └── dac
-            ├── aoml
-            ├── ...
-            ├── coriolis
-            ├── ...
-            ├── meds
-            └── nmdis
-
-        Examples:
-        >>> check_gdac_path("https://data-argo.ifremer.fr")  # True
-        >>> check_gdac_path("ftp://ftp.ifremer.fr/ifremer/argo") # True
-        >>> check_gdac_path("ftp://usgodae.org/pub/outgoing/argo") # True
-        >>> check_gdac_path("/home/ref-argo/gdac") # True
-        >>> check_gdac_path("https://www.ifremer.fr") # False
-        >>> check_gdac_path("ftp://usgodae.org/pub/outgoing") # False
-
-        Parameters
-        ----------
-        path: str
-            Path name to check, including access protocol
-        errors: str
-            "ignore" or "raise" (or "warn")
-
-        Returns
-        -------
-        checked: boolean
-            True if at least one DAC folder is found under path/dac/<dac_name>
-            False otherwise
+def check_gdac_path(path, errors="ignore"):  # noqa: C901
+    """Check if a path has the expected GDAC ftp structure
+
+    Check if a path is structured like:
+    .
+    └── dac
+        ├── aoml
+        ├── ...
+        ├── coriolis
+        ├── ...
+        ├── meds
+        └── nmdis
+
+    Examples:
+    >>> check_gdac_path("https://data-argo.ifremer.fr")  # True
+    >>> check_gdac_path("ftp://ftp.ifremer.fr/ifremer/argo") # True
+    >>> check_gdac_path("ftp://usgodae.org/pub/outgoing/argo") # True
+    >>> check_gdac_path("/home/ref-argo/gdac") # True
+    >>> check_gdac_path("https://www.ifremer.fr") # False
+    >>> check_gdac_path("ftp://usgodae.org/pub/outgoing") # False
+
+    Parameters
+    ----------
+    path: str
+        Path name to check, including access protocol
+    errors: str
+        "ignore" or "raise" (or "warn")
+
+    Returns
+    -------
+    checked: boolean
+        True if at least one DAC folder is found under path/dac/<dac_name>
+        False otherwise
     """
     # Create a file system for this path
     if split_protocol(path)[0] is None:
-        fs = fsspec.filesystem('file')
-    elif split_protocol(path)[0] in ['https', 'http']:
-        fs = fsspec.filesystem('http')
-    elif 'ftp' in split_protocol(path)[0]:
+        fs = fsspec.filesystem("file")
+    elif split_protocol(path)[0] in ["https", "http"]:
+        fs = fsspec.filesystem("http")
+    elif "ftp" in split_protocol(path)[0]:
         try:
             host = urlparse(path).hostname
             port = 0 if urlparse(path).port is None else urlparse(path).port
-            fs = fsspec.filesystem('ftp', host=host, port=port)
+            fs = fsspec.filesystem("ftp", host=host, port=port)
         except gaierror:
-            if errors == 'raise':
+            if errors == "raise":
                 raise FtpPathError("Can't get address info (GAIerror) on '%s'" % host)
             elif errors == "warn":
                 warnings.warn("Can't get address info (GAIerror) on '%s'" % host)
                 return False
             else:
                 return False
     else:
-        raise FtpPathError("Unknown protocol for an Argo GDAC host: %s" % split_protocol(path)[0])
+        raise FtpPathError(
+            "Unknown protocol for an Argo GDAC host: %s" % split_protocol(path)[0]
+        )
 
     # dacs = [
     #     "aoml",
@@ -310,7 +322,10 @@ def check_gdac_path(path, errors='ignore'):  # noqa: C901
         return True
 
     elif errors == "raise":
-        raise FtpPathError("This path is not GDAC compliant (no `dac` folder with legitimate sub-folder):\n%s" % path)
+        raise FtpPathError(
+            "This path is not GDAC compliant (no `dac` folder with legitimate sub-folder):\n%s"
+            % path
+        )
 
     elif errors == "warn":
         warnings.warn("This path is not GDAC compliant:\n%s" % path)

argopy/related/argo_documentation.py

@@ -75,7 +75,7 @@ def parse(self, file):
                         else:
                             # print("-", line)
                             record[tag].append(line)
-                    except UnboundLocalError as e:
+                    except UnboundLocalError:
                         pass
                 elif len(line) == 2:
                     record[line] = []

argopy/related/reference_tables.py

@@ -31,9 +31,6 @@ class ArgoNVSReferenceTables:
 
     valid_ref = [
         "R01",
-        "RR2",
-        "RD2",
-        "RP2",
         "R03",
         "R04",
         "R05",
@@ -46,8 +43,6 @@ class ArgoNVSReferenceTables:
         "R12",
         "R13",
         "R15",
-        "RMC",
-        "RTV",
         "R16",
         "R18",
         "R19",
@@ -60,9 +55,12 @@ class ArgoNVSReferenceTables:
         "R26",
         "R27",
         "R28",
-        "R29",
-        "R30",
         "R40",
+        "RD2",
+        "RMC",
+        "RP2",
+        "RR2",
+        "RTV",
     ]
     """List of all available Reference Tables"""