Merge pull request #275 from euroargodev/v0.1.14-pre

Prepare for "v0.1.14-pre Duck Release 🦆"

HOW_TO_RELEASE.md

@@ -1,15 +1,12 @@
 # Setup
 
-- [ ] Create a new branch for this release: ``git checkout -b releasev0.1.14``
+- [ ] Create a new branch for this release: ``git checkout -b releasev0.X.Y``
 - [ ] Increase release version in ``./setup.py``
 - [ ] Update release version in ``./docs/whats-new.rst``
 - [ ] 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+) 
 
 # Prepare code for release
 
-- [ ] 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
-
 ## Code clean-up
 - [ ] 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
@@ -37,5 +34,6 @@ Choose the release tag v0.X.Y, fill in the release title and click on the `Auto-
 This will trigger the [publish Github action](https://github.com/euroargodev/argopy/blob/master/.github/workflows/pythonpublish.yml) that will push the release on [Pypi](https://pypi.org/project/argopy/#history).
 
 # CI tests / RTD build results
-[![CI tests](https://github.com/euroargodev/argopy/actions/workflows/pytests.yml/badge.svg?branch=releasev0.X.Y)](https://github.com/euroargodev/argopy/actions/workflows/pytests.yml) [![CI tests (MacOs)](https://github.com/euroargodev/argopy/actions/workflows/pytests_mac.yml/badge.svg?branch=releasev0.X.Y)](https://github.com/euroargodev/argopy/actions/workflows/pytests_mac.yml) [![CI tests (Windows)](https://github.com/euroargodev/argopy/actions/workflows/pytests_windows.yml/badge.svg?branch=releasev0.X.Y)](https://github.com/euroargodev/argopy/actions/workflows/pytests_windows.yml) [![CI tests Upstream](https://github.com/euroargodev/argopy/actions/workflows/pytests-upstream.yml/badge.svg?branch=releasev0.X.Y)](https://github.com/euroargodev/argopy/actions/workflows/pytests-upstream.yml)
+[![CI tests](https://github.com/euroargodev/argopy/actions/workflows/pytests.yml/badge.svg?branch=releasev0.X.Y)](https://github.com/euroargodev/argopy/actions/workflows/pytests.yml) 
+[![CI tests Upstream](https://github.com/euroargodev/argopy/actions/workflows/pytests-upstream.yml/badge.svg?branch=releasev0.X.Y)](https://github.com/euroargodev/argopy/actions/workflows/pytests-upstream.yml)
 [![Documentation Status](https://readthedocs.org/projects/argopy/badge/?version=releasev0.X.Y)](https://argopy.readthedocs.io/en/releasev0.X.Y)

argopy/__init__.py

@@ -32,8 +32,8 @@
 from .utilities import TopoFetcher, ArgoNVSReferenceTables, OceanOPSDeployments, ArgoDocs  # noqa: E402
 from .utilities import monitor_status as status  # noqa: E402
 from .options import set_options  # noqa: E402
-from .data_fetchers import CTDRefDataFetcher
-from .stores import ArgoIndex
+from .data_fetchers import CTDRefDataFetcher  # noqa: E402
+from .stores import ArgoIndex  # noqa: E402
 
 #
 __all__ = (

argopy/data_fetchers/argovis_data.py

@@ -15,7 +15,7 @@
 
 from argopy.stores import httpstore
 from argopy.options import OPTIONS
-from argopy.utilities import list_standard_variables, format_oneline, Chunker
+from argopy.utilities import format_oneline, Chunker
 from argopy.errors import DataNotFound
 
 

argopy/data_fetchers/erddap_data.py

@@ -19,7 +19,7 @@
 
 from .proto import ArgoDataFetcherProto
 from argopy.options import OPTIONS
-from argopy.utilities import list_standard_variables, Chunker, format_oneline
+from argopy.utilities import Chunker, format_oneline
 from argopy.stores import httpstore
 from ..errors import ErddapServerError
 from aiohttp import ClientResponseError

argopy/data_fetchers/erddap_refdata.py

@@ -4,7 +4,7 @@
 import xarray as xr
 from .erddap_data import ErddapArgoDataFetcher
 from argopy.options import OPTIONS
-from argopy.utilities import Chunker, doc_inherit
+from argopy.utilities import Chunker
 from argopy.stores import httpstore_erddap_auth
 import logging
 

argopy/data_fetchers/proto.py

@@ -7,6 +7,7 @@
 from ..plot import dashboard
 from ..utilities import list_standard_variables
 
+
 class ArgoDataFetcherProto(ABC):
     @abstractmethod
     def to_xarray(self, *args, **kwargs) -> xarray.Dataset:

argopy/errors.py

@@ -24,6 +24,7 @@ class ErddapPathError(ValueError):
 
     pass
 
+
 class NetCDF4FileNotFoundError(FileNotFoundError):
     """Raise when NETCDF4 file not found."""
 
@@ -132,7 +133,8 @@ class ErddapHTTPUnauthorized(APIServerError):
 
     pass
 
+
 class ErddapHTTPNotFound(APIServerError):
-    """Raise when erddap ressource is not found"""
+    """Raise when erddap resource is not found"""
 
     pass

argopy/stores/filesystems.py

@@ -1160,7 +1160,7 @@ def __init__(self,
         else:
             self._login_page = login
 
-        self._login_auto = auto  # Should we try to log-in automatically at instanciation ?
+        self._login_auto = auto  # Should we try to log-in automatically at instantiation ?
 
         self._login_payload = payload.copy()
         if "user" in self._login_payload and self._login_payload['user'] is None:

argopy/utilities.py

@@ -495,8 +495,8 @@ def show_versions(file=sys.stdout, conda=False):  # noqa: C901
             ("fsspec", lambda mod: mod.__version__),
             ("aiohttp", lambda mod: mod.__version__),
             ("packaging", lambda mod: mod.__version__),  # will come with xarray, Using 'version' to make API compatible with several fsspec releases
-            ("toolz", lambda mod: mod.__version__),
             ("requests", lambda mod: mod.__version__),
+            ("toolz", lambda mod: mod.__version__),
         ]),
         'ext.util': sorted([
             ("gsw", lambda mod: mod.__version__),   # Used by xarray accessor to compute new variables
@@ -534,7 +534,9 @@ def show_versions(file=sys.stdout, conda=False):  # noqa: C901
             ("pytest_env", lambda mod: mod.__version__),  # will come with pandas
             ("pytest_cov", lambda mod: mod.__version__),  # will come with pandas
             ("pytest_localftpserver", lambda mod: mod.__version__),  # will come with pandas
-            ("setuptools", lambda mod: mod.__version__),  # Provides: pkg_resources
+            ("pytest_reportlog", lambda mod: mod.__version__),  # will come with pandas
+            ("setuptools", lambda mod: mod.__version__),
+            ("aiofiles", lambda mod: mod.__version__),
             ("sphinx", lambda mod: mod.__version__),
         ]),
     }
@@ -3920,133 +3922,133 @@ class ArgoDocs:
     """
     _catalogue = [
         {
-            "categorie": "Argo data formats",
+            "category": "Argo data formats",
             "title": "Argo user's manual",
             "doi": "10.13155/29825",
             "id": 29825
         },
         {
-            "categorie": "Quality control",
+            "category": "Quality control",
             "title": "Argo Quality Control Manual for CTD and Trajectory Data",
             "doi": "10.13155/33951",
             "id": 33951
         },
         {
-            "categorie": "Quality control",
+            "category": "Quality control",
             "title": "Argo quality control manual for dissolved oxygen concentration",
             "doi": "10.13155/46542",
             "id": 46542
         },
         {
-            "categorie": "Quality control",
+            "category": "Quality control",
             "title": "Argo quality control manual for biogeochemical data",
             "doi": "10.13155/40879",
             "id": 40879
         },
         {
-            "categorie": "Quality control",
+            "category": "Quality control",
             "title": "BGC-Argo quality control manual for the Chlorophyll-A concentration",
             "doi": "10.13155/35385",
             "id": 35385
         },
         {
-            "categorie": "Quality control",
+            "category": "Quality control",
             "title": "BGC-Argo quality control manual for nitrate concentration",
             "doi": "10.13155/84370",
             "id": 84370
         },
         {
-            "categorie": "Quality control",
+            "category": "Quality control",
             "title": "Quality control for BGC-Argo radiometry",
             "doi": "10.13155/62466",
             "id": 62466
         },
         {
-            "categorie": "Cookbooks",
+            "category": "Cookbooks",
             "title": "Argo DAC profile cookbook",
             "doi": "10.13155/41151",
             "id": 41151
         },
         {
-            "categorie": "Cookbooks",
+            "category": "Cookbooks",
             "title": "Argo DAC trajectory cookbook",
             "doi": "10.13155/29824",
             "id": 29824
         },
         {
-            "categorie": "Cookbooks",
+            "category": "Cookbooks",
             "title": "DMQC Cookbook for Core Argo parameters",
             "doi": "10.13155/78994",
             "id": 78994
         },
         {
-            "categorie": "Cookbooks",
+            "category": "Cookbooks",
             "title": "Processing Argo oxygen data at the DAC level",
             "doi": "10.13155/39795",
             "id": 39795
         },
         {
-            "categorie": "Cookbooks",
+            "category": "Cookbooks",
             "title": "Processing Bio-Argo particle backscattering at the DAC level",
             "doi": "10.13155/39459",
             "id": 39459
         },
         {
-            "categorie": "Cookbooks",
+            "category": "Cookbooks",
             "title": "Processing BGC-Argo chlorophyll-A concentration at the DAC level",
             "doi": "10.13155/39468",
             "id": 39468
         },
         {
-            "categorie": "Cookbooks",
+            "category": "Cookbooks",
             "title": "Processing Argo measurement timing information at the DAC level",
             "doi": "10.13155/47998",
             "id": 47998
         },
         {
-            "categorie": "Cookbooks",
+            "category": "Cookbooks",
             "title": "Processing BGC-Argo CDOM concentration at the DAC level",
             "doi": "10.13155/54541",
             "id": 54541
         },
         {
-            "categorie": "Cookbooks",
+            "category": "Cookbooks",
             "title": "Processing Bio-Argo nitrate concentration at the DAC Level",
             "doi": "10.13155/46121",
             "id": 46121
         },
         {
-            "categorie": "Cookbooks",
+            "category": "Cookbooks",
             "title": "Processing BGC-Argo Radiometric data at the DAC level",
             "doi": "10.13155/51541",
             "id": 51541
         },
         {
-            "categorie": "Cookbooks",
+            "category": "Cookbooks",
             "title": "Processing BGC-Argo pH data at the DAC level",
             "doi": "10.13155/57195",
             "id": 57195
         },
         {
-            "categorie": "Cookbooks",
+            "category": "Cookbooks",
             "title": "Description of the Argo GDAC File Checks: Data Format and Consistency Checks",
             "doi": "10.13155/46120",
             "id": 46120
         },
         {
-            "categorie": "Cookbooks",
+            "category": "Cookbooks",
             "title": "Description of the Argo GDAC File Merge Process",
             "doi": "10.13155/52154",
             "id": 52154
         },
         {
-            "categorie": "Cookbooks",
+            "category": "Cookbooks",
             "title": "BGC-Argo synthetic profile file processing and format on Coriolis GDAC",
             "doi": "10.13155/55637",
             "id": 55637
         },
         {
-            "categorie": "Cookbooks",
+            "category": "Cookbooks",
             "title": "Argo GDAC cookbook",
             "doi": "10.13155/46202",
             "id": 46202
@@ -4107,7 +4109,7 @@ def __init__(self, docid=None):
             if docid in [doc['id'] for doc in self._catalogue]:
                 self.docid = docid
             else:
-                raise ValueError("Unknow document id")
+                raise ValueError("Unknown document id")
 
     def __repr__(self):
         summary = ["<argopy.ArgoDocs>"]

ci/requirements/py3.8-all-free.yml

@@ -48,5 +48,6 @@ dependencies:
   - pytest-env
   - pytest-localftpserver
   - pytest-reportlog
+  - aiofiles
   - setuptools
 #  - sphinx

ci/requirements/py3.8-all-pinned.yml

@@ -6,10 +6,10 @@ dependencies:
 
 # CORE:
   - aiohttp = 3.8.4
-  - erddapy = 1.2.1
-  - fsspec = 2023.3.0
+  - erddapy = 2.0.1
+  - fsspec = 2023.5.0
   - netCDF4 = 1.6.3
-  - packaging = 23.0
+  - packaging = 23.1
   - scipy = 1.10.1
   - toolz = 0.12.0
   - xarray = 2023.1.0
@@ -20,34 +20,35 @@ dependencies:
   - zarr = 2.14.2
 
 # EXT.PERF:
-  - dask = 2023.3.1
-  - distributed = 2023.3.1
-  - pyarrow = 11.0.0
+  - dask = 2023.5.0
+  - distributed = 2023.5.0
+  - pyarrow = 12.0.0
 
 # EXT.PLOT:
-  - IPython = 8.11.0
+  - IPython = 8.12.2
   - cartopy = 0.21.1
-  - ipykernel = 6.22.0
-  - ipywidgets = 8.0.5
+  - ipykernel = 6.23.1
+  - ipywidgets = 8.0.6
   - matplotlib = 3.7.1
   - seaborn = 0.12.2
 
 # DEV:
-  - black = 23.1.0
+  - black = 23.3.0
   - bottleneck = 1.3.7
-  - cfgrib = 0.9.10.3
+  - cfgrib = 0.9.10.4
   - cftime = 1.6.2
 #  - conda = -
   - flake8 = 6.0.0
 #  - nc-time-axis = -
-  - numpy = 1.24.2
+  - numpy = 1.24.3
   - pandas = 1.5.3
-  - pip = 23.0.1
-  - pytest = 7.2.2
-  - pytest-cov = 4.0.0
+  - pip = 23.1.2
+  - pytest = 7.3.1
+  - pytest-cov = 4.1.0
   - pytest-env = 0.8.1
   - pytest-localftpserver = 1.1.4
-  - aiofiles=0.7.0  
-  - setuptools = 67.6.0
+  - pytest-reportlog
+  - aiofiles=0.7.0
+  - setuptools = 67.7.2
 #  - sphinx = -