Merge branch 'master' into other-major-breaking-refactoring

.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:

.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

HOW_TO_RELEASE.md

@@ -3,7 +3,8 @@
 - [ ] Create a new branch for this release: ``git checkout -b releasev0.X.Y``
 - [ ] Update release version in ``./docs/whats-new.rst``
 - [ ] Increase release version in ``./setup.py``
-- [ ] Create a PR to prepare it, name it with one of the [Nature emoji](https://www.webfx.com/tools/emoji-cheat-sheet/#tabs-3) and make sure it was [never used before](https://github.com/euroargodev/argopy/pulls?q=is%3Apr+label%3Arelease+) 
+- [ ] Create a PR to prepare it, name it with one of the [Nature emoji](https://www.webfx.com/tools/emoji-cheat-sheet/#tabs-3) and make sure it was [never used before](https://github.com/euroargodev/argopy/pulls?q=is%3Apr+label%3Arelease+)
+- [ ] [Activate RTD build for this branch](https://app.readthedocs.org/dashboard/argopy/version/create/)
 
 # Prepare code for release
 
@@ -14,7 +15,19 @@
   - [ ] If code is marked as deprecated since version = v0.X.Y-2 : delete code (code will raise an error)
 - [ ] Update the documentation according to new deprecations
 
-## Code clean-up
+## Update static content
+- [ ] Update CI tests data used by mocked ftp and http servers. Use CLI [citests_httpdata_manager](https://github.com/euroargodev/argopy/blob/master/cli/citests_httpdata_manager):
+  ```bash
+  cd cli
+  ./citests_httpdata_manager -a clear --force --refresh
+  ./citests_httpdata_manager -a download
+  ./citests_httpdata_manager -a check
+  ```
+- [ ] Update list of valid Reference tables from the [NVS server](https://vocab.nerc.ac.uk/collection/?filter=Argo)
+- [ ] Update [static assets files](https://github.com/euroargodev/argopy/tree/master/argopy/static/assets)
+- [ ] Update the [cheatsheet PDF](https://github.com/euroargodev/argopy/blob/master/docs/_static/argopy-cheatsheet.pdf) with all new release features
+
+## Code clean-up and update
 - [ ] Run [codespell](https://github.com/codespell-project/codespell) from repo root and fix errors: ``codespell -q 2``
 - [ ] Run [flake8](https://github.com/PyCQA/flake8) from repo root and fix errors
 
@@ -23,7 +36,7 @@
 - [ ] Update pinned dependencies versions in ``./ci/requirements/py*-*-pinned.yml`` environment files using [upstream CI tests](https://github.com/euroargodev/argopy/actions/workflows/pytests-upstream.yml) information
 - [ ] Possibly update ``./requirements.txt`` and ``./docs/requirements.txt`` if the oldest dependencies versions were upgraded
 - [ ] Make sure that all CI tests are passed
-- [ ] [Activate](https://readthedocs.org/projects/argopy/versions/) and make sure the documentation for the release branch is [built on RTD](https://readthedocs.org/projects/argopy/builds/)
+- [ ] Make sure the documentation for this release branch is [built on RTD](https://readthedocs.org/projects/argopy/builds/)
 
 ## Preparation conclusion
 - [ ] Merge this PR to master

argopy/data_fetchers/argovis_data.py

@@ -528,7 +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:
@@ -556,6 +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)

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

@@ -1,4 +1,9 @@
 """A bunch of custom errors used in argopy."""
+from typing import List
+import warnings
+import logging
+
+log = logging.getLogger("argopy.errors")
 
 class NoData(ValueError):
     """Raise for no data"""
@@ -152,3 +157,48 @@ class ErddapHTTPNotFound(APIServerError):
     """Raise when erddap resource is not found"""
 
     pass
+
+
+class OptionDeprecatedWarning(DeprecationWarning):
+    """When an option being deprecated is used
+
+    This is a class to emit a warning when an option being deprecated is used.
+
+    Parameters
+    ----------
+    reason: str, optional, default=None
+        Text message to send with deprecation warning
+    version: str, optional, default=None
+    ignore_caller: List, optional, default=[]
+    """
+    def __init__(self, reason: str = None, version: str = None, ignore_caller: List = []):
+        import inspect
+        ignore_caller = [ignore_caller]
+
+        if isinstance(reason, str):
+
+            fmt = "\nCall to deprecated option: {reason}"
+            if version is not None:
+                fmt = "%s -- Deprecated since version {version}" % fmt
+
+            issue_deprec = True
+            stack = inspect.stack()
+            for s in stack:
+                if "<module>" in s.function:
+                    break
+                elif s.function in ignore_caller:
+                    issue_deprec = False
+
+            if issue_deprec:
+                warnings.simplefilter("always", DeprecationWarning)
+                warnings.warn(
+                    fmt.format(reason=reason, version=version),
+                    category=DeprecationWarning,
+                    stacklevel=2,
+                )
+                warnings.simplefilter("default", DeprecationWarning)
+            else:
+                log.warning(fmt.format(reason=reason, version=version))
+
+        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
+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,
@@ -166,8 +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",
+            )
 
     def __repr__(self):
         para = (
@@ -299,7 +306,7 @@ def domain(self):
 
     @property
     def mission(self):
-        if self._dataset_id == 'bgc':
+        if self._dataset_id == "bgc":
             return "BGC"
         else:
             return "core+deep"
@@ -592,18 +599,21 @@ def to_index(self, full: bool = False, coriolis_id: bool = False) -> pd.DataFram
         :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)
@@ -626,7 +636,9 @@ 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()
@@ -673,7 +685,7 @@ 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
 
@@ -691,7 +703,7 @@ def fc(row):
         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.

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"""
 

argopy/static/assets/admt_documentation_catalogue.json

@@ -1,7 +1,7 @@
 {
   "name": "ADMT documentation catalogue",
   "long_name": "Titles and DOIs of all the official ADMT documentation",
-  "last_update": "2024-09-12T14:13:10.643203+00:00",
+  "last_update": "2024-09-20T09:27:55.161297+00:00",
   "data": {
     "catalogue": [
       {

argopy/static/assets/api_coriolis_parameter_codes.json

@@ -1,7 +1,7 @@
 {
   "name": "parameters",
   "long_name": "All valid requests to https://api-coriolis.ifremer.fr/legacy/parameter?code={code}",
-  "last_update": "2024-09-12T14:13:10.597080+00:00",
+  "last_update": "2024-09-20T09:27:55.145057+00:00",
   "data": {
     "valid_codes": [
       "9",

argopy/static/assets/data_types.json

@@ -1,7 +1,7 @@
 {
   "name": "data_types",
   "long_name": "Expected data types of Argo variables",
-  "last_update": "2024-09-12T14:12:40.949768+00:00",
+  "last_update": "2024-09-20T09:26:28.473595+00:00",
   "data": {
     "str": [
       "PLATFORM_NUMBER",

argopy/static/assets/institutions.json

@@ -1,7 +1,7 @@
 {
   "name": "institutions",
   "long_name": "Institution names from Argo reference table 4",
-  "last_update": "2024-09-12T14:12:41.637174+00:00",
+  "last_update": "2024-09-20T09:26:28.990073+00:00",
   "data": {
     "institutions": {
       "PL": "IOPAN, Institute of Oceanology Polish Academy of Science",

argopy/static/assets/profilers.json

@@ -1,7 +1,7 @@
 {
   "name": "profilers",
   "long_name": "Profiler codes and description from Argo reference table 8",
-  "last_update": "2024-09-12T14:12:42.118648+00:00",
+  "last_update": "2024-09-20T09:26:30.350138+00:00",
   "data": {
     "profilers": {
       "841": "PROVOR float with SBE conductivity sensor",

argopy/static/assets/variables_bgc_synthetic.json

@@ -1,7 +1,7 @@
 {
   "name": "BGC synthetic netcdf files variables",
   "long_name": "Variables from the Ifremer Erddap ArgoFloats-synthetic-BGC dataset based on GDAC synthetic netcdf files",
-  "last_update": "2024-09-12T14:13:10.711233+00:00",
+  "last_update": "2024-09-20T09:27:55.354835+00:00",
   "data": {
     "variables": [
       "BBP470",