Merge branch 'development' into tweak-contributor-doc

icesat2py · Aug 26, 2024 · 59d4355 · 59d4355
2 parents 19e5a5b + e491c84
commit 59d4355
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diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -470,6 +470,41 @@
       "contributions": [
         "ideas"
       ]
+    },
+    {
+      "login": "cclauss",
+      "name": "Christian Clauss",
+      "avatar_url": "https://avatars.githubusercontent.com/u/3709715?v=4",
+      "profile": "https://github.com/cclauss",
+      "contributions": [
+        "maintenance",
+        "review",
+        "tool"
+      ]
+    },
+    {
+      "login": "jrenrut",
+      "name": "Jeremy Turner",
+      "avatar_url": "https://avatars.githubusercontent.com/u/42989238?v=4",
+      "profile": "https://github.com/jrenrut",
+      "contributions": [
+        "bug",
+        "code"
+      ]
+    },
+    {
+      "login": "mfisher87",
+      "name": "Matt Fisher",
+      "avatar_url": "https://avatars.githubusercontent.com/u/3608264?v=4",
+      "profile": "https://mfisher87.github.io/",
+      "contributions": [
+        "bug",
+        "code",
+        "doc",
+        "maintenance",
+        "test",
+        "infra"
+      ]
     }
   ],
   "contributorsPerLine": 7,

diff --git a/CONTRIBUTORS.rst b/CONTRIBUTORS.rst
diff --git a/README.rst b/README.rst
@@ -85,6 +85,32 @@ Alternatively, you can also install icepyx using `pip <https://pip.pypa.io/en/st
 More detailed instructions for installing `icepyx` can be found at
 https://icepyx.readthedocs.io/en/latest/getting_started/install.html
 
+Quick Start
+-----------
+
+.. code-block:: python
+
+   import icepyx as ipx
+   query = ipx.Query(
+       # Collection short name
+       "ATL06",
+       # Bounding box
+       [-55, 68, -48, 71],
+       # Time bounds
+       ['2019-02-20','2019-02-28'],
+   )
+   query.download_granules('/tmp/icepyx')
+
+.. code-block:: bash
+
+   $ ls -1 /tmp/icepyx/
+   processed_ATL06_20190221121851_08410203_006_02.h5
+   processed_ATL06_20190222010344_08490205_006_02.h5
+   processed_ATL06_20190225121032_09020203_006_02.h5
+   processed_ATL06_20190226005526_09100205_006_02.h5
+
+See the examples below for more things `icepyx` can do!
+
 
 Examples (Jupyter Notebooks)
 ----------------------------

diff --git a/doc/source/user_guide/documentation/classes_dev_uml.svg b/doc/source/user_guide/documentation/classes_dev_uml.svg
diff --git a/doc/source/user_guide/documentation/classes_user_uml.svg b/doc/source/user_guide/documentation/classes_user_uml.svg
diff --git a/doc/sphinxext/announce.py b/doc/sphinxext/announce.py
@@ -77,10 +77,7 @@ def get_authors(revision_range):
         # e.g. v1.0.1|HEAD
         maybe_tag, head = cur_release.split("|")
         assert head == "HEAD"
-        if maybe_tag in this_repo.tags:
-            cur_release = maybe_tag
-        else:
-            cur_release = head
+        cur_release = maybe_tag if maybe_tag in this_repo.tags else head
         revision_range = f"{lst_release}..{cur_release}"
 
     # authors, in current release and previous to current release.
@@ -125,7 +122,7 @@ def get_authors(revision_range):
     #     pre.discard("Homu")
 
     # Append '+' to new authors.
-    authors = [s + " +" for s in cur - pre] + [s for s in cur & pre]
+    authors = [s + " +" for s in cur - pre] + list(cur & pre)
     authors.sort()
     return authors
 

diff --git a/icepyx/core/APIformatting.py b/icepyx/core/APIformatting.py
@@ -73,7 +73,7 @@ def _fmt_readable_granules(dset, **kwds):
     # list of readable granule names
     readable_granule_list = []
     # if querying either by 91-day orbital cycle or RGT
-    if "cycles" in kwargs.keys() or "tracks" in kwargs.keys():
+    if "cycles" in kwargs or "tracks" in kwargs:
         # default character wildcards for cycles and tracks
         kwargs.setdefault("cycles", ["??"])
         kwargs.setdefault("tracks", ["????"])
@@ -110,7 +110,7 @@ def _fmt_var_subset_list(vdict):
     """
 
     subcover = ""
-    for vn in vdict.keys():
+    for vn in vdict:
         vpaths = vdict[vn]
         for vpath in vpaths:
             subcover += "/" + vpath + ","
@@ -298,9 +298,9 @@ def _check_valid_keys(self):
         # if self._wanted == None:
         #     raise ValueError("No desired parameter list was passed")
 
-        val_list = list(set(val for lis in self.poss_keys.values() for val in lis))
+        val_list = list({val for lis in self.poss_keys.values() for val in lis})
 
-        for key in self.fmted_keys.keys():
+        for key in self.fmted_keys:
             assert key in val_list, (
                 "An invalid key (" + key + ") was passed. Please remove it using `del`"
             )
@@ -317,7 +317,7 @@ def check_req_values(self):
         ), "You cannot call this function for your parameter type"
         reqkeys = self.poss_keys[self._reqtype]
 
-        if all(keys in self.fmted_keys.keys() for keys in reqkeys):
+        if all(keys in self.fmted_keys for keys in reqkeys):
             assert all(
                 self.fmted_keys.get(key, -9999) != -9999 for key in reqkeys
             ), "One of your formatted parameters is missing a value"
@@ -337,7 +337,7 @@ def check_values(self):
         spatial_keys = self.poss_keys["spatial"]
 
         # not the most robust check, but better than nothing...
-        if any(keys in self._fmted_keys.keys() for keys in spatial_keys):
+        if any(keys in self._fmted_keys for keys in spatial_keys):
             assert any(
                 self.fmted_keys.get(key, -9999) != -9999 for key in spatial_keys
             ), "One of your formatted parameters is missing a value"
@@ -410,13 +410,13 @@ def build_params(self, **kwargs):
                 opt_keys = self.poss_keys["optional"]
 
                 for key in opt_keys:
-                    if key == "Coverage" and key in kwargs.keys():
+                    if key == "Coverage" and key in kwargs:
                         # DevGoal: make there be an option along the lines of Coverage=default, which will get the default variables for that product without the user having to input is2obj.build_wanted_wanted_var_list as their input value for using the Coverage kwarg
                         self._fmted_keys.update(
                             {key: _fmt_var_subset_list(kwargs[key])}
                         )
                     elif (key == "temporal" or key == "time") and (
-                        "start" in kwargs.keys() and "end" in kwargs.keys()
+                        "start" in kwargs and "end" in kwargs
                     ):
                         self._fmted_keys.update(
                             _fmt_temporal(kwargs["start"], kwargs["end"], key)

diff --git a/icepyx/core/auth.py b/icepyx/core/auth.py
@@ -107,11 +107,9 @@ def set_s3_creds():
 
         # Only generate s3login_credentials the first time credentials are accessed, or if an hour
         # has passed since the last login
-        if self._s3login_credentials is None:
-            set_s3_creds()
-        elif (datetime.datetime.now() - self._s3_initial_ts) >= datetime.timedelta(
-            hours=1
-        ):
+        if self._s3login_credentials is None or (
+            datetime.datetime.now() - self._s3_initial_ts
+        ) >= datetime.timedelta(hours=1):
             set_s3_creds()
         return self._s3login_credentials
 

diff --git a/icepyx/core/granules.py b/icepyx/core/granules.py
@@ -75,14 +75,13 @@ def gran_IDs(grans, ids=False, cycles=False, tracks=False, dates=False, cloud=Fa
         if cloud is True:
             try:
                 for link in gran["links"]:
-                    if link["href"].startswith("s3") and link["href"].endswith(
-                        (".h5", "nc")
-                    ):
-                        gran_s3urls.append(link["href"])
+                    href = link["href"]
+                    if href.startswith("s3") and href.endswith((".h5", "nc")):
+                        gran_s3urls.append(href)
             except KeyError:
                 pass
 
-        if any([param is True for param in [cycles, tracks, dates]]):
+        if any(param is True for param in [cycles, tracks, dates]):
             # PRD: ICESat-2 product
             # HEM: Sea Ice Hemisphere flag
             # YY,MM,DD,HH,MN,SS: Year, Month, Day, Hour, Minute, Second

diff --git a/icepyx/core/query.py b/icepyx/core/query.py
@@ -126,7 +126,7 @@ def __init__(
         **kwargs,
     ):
         # validate & init spatial extent
-        if "xdateline" in kwargs.keys():
+        if "xdateline" in kwargs:
             self._spatial = spat.Spatial(spatial_extent, xdateline=kwargs["xdateline"])
         else:
             self._spatial = spat.Spatial(spatial_extent)
@@ -637,7 +637,7 @@ def subsetparams(self, **kwargs):
         else:
             # If the user has supplied a subset list of variables, append the
             # icepyx required variables to the Coverage dict
-            if "Coverage" in kwargs.keys():
+            if "Coverage" in kwargs:
                 var_list = [
                     "orbit_info/sc_orient",
                     "orbit_info/sc_orient_time",
@@ -653,7 +653,7 @@ def subsetparams(self, **kwargs):
                 ]
                 # Add any variables from var_list to Coverage that are not already included
                 for var in var_list:
-                    if var not in kwargs["Coverage"].keys():
+                    if var not in kwargs["Coverage"]:
                         kwargs["Coverage"][var.split("/")[-1]] = [var]
 
             if self._subsetparams is None:
@@ -741,9 +741,7 @@ def granules(self):
         <icepyx.core.granules.Granules at [location]>
         """
 
-        if not hasattr(self, "_granules"):
-            self._granules = Granules()
-        elif self._granules is None:
+        if not hasattr(self, "_granules") or self._granules is None:
             self._granules = Granules()
 
         return self._granules
@@ -869,8 +867,8 @@ def show_custom_options(self, dictview=False):
         ]
 
         try:
-            all(key in self._cust_options.keys() for key in keys)
-        except AttributeError or KeyError:
+            all(key in self._cust_options for key in keys)
+        except (AttributeError, KeyError):
             self._cust_options = is2ref._get_custom_options(
                 self.session, self.product, self._version
             )
@@ -999,7 +997,7 @@ def order_granules(self, verbose=False, subset=True, email=False, **kwargs):
         if self._reqparams._reqtype == "search":
             self._reqparams._reqtype = "download"
 
-        if "email" in self._reqparams.fmted_keys.keys() or email is False:
+        if "email" in self._reqparams.fmted_keys or email is False:
             self._reqparams.build_params(**self._reqparams.fmted_keys)
         elif email is True:
             user_profile = self.auth.get_user_profile()
@@ -1022,7 +1020,7 @@ def order_granules(self, verbose=False, subset=True, email=False, **kwargs):
             self.granules
 
         # Place multiple orders, one per granule, if readable_granule_name is used.
-        if "readable_granule_name[]" in self.CMRparams.keys():
+        if "readable_granule_name[]" in self.CMRparams:
             gran_name_list = self.CMRparams["readable_granule_name[]"]
             tempCMRparams = self.CMRparams
             if len(gran_name_list) > 1:

diff --git a/icepyx/core/read.py b/icepyx/core/read.py
@@ -120,7 +120,7 @@ def _parse_source(data_source, glob_kwargs={}) -> list:
         # if data_source is a directory glob search the directory and assign to _filelist
         data_source = os.path.join(data_source, "*")
         filelist = glob.glob(data_source, **glob_kwargs)
-    elif isinstance(data_source, str) or isinstance(data_source, Path):
+    elif isinstance(data_source, (Path, str)):
         if data_source.startswith("s3"):
             # if the string is an s3 path put it in the _filelist without globbing
             filelist = [data_source]
@@ -661,11 +661,11 @@ def _build_dataset_template(self, file):
         """
 
         is2ds = xr.Dataset(
-            coords=dict(
-                gran_idx=[np.uint64(999999)],
-                source_file=(["gran_idx"], [file]),
-            ),
-            attrs=dict(data_product=self.product),
+            coords={
+                "gran_idx": [np.uint64(999999)],
+                "source_file": (["gran_idx"], [file]),
+            },
+            attrs={"data_product": self.product},
         )
         return is2ds
 
@@ -740,7 +740,7 @@ def _build_single_file_dataset(self, file, groups_list):
             "ATL23",
         ]:
             wanted_grouponly_set = set(wanted_groups_tiered[0])
-            wanted_groups_list = list(sorted(wanted_grouponly_set))
+            wanted_groups_list = sorted(wanted_grouponly_set)
             if len(wanted_groups_list) == 1:
                 is2ds = self._read_single_grp(file, grp_path=wanted_groups_list[0])
             else:

diff --git a/icepyx/core/spatial.py b/icepyx/core/spatial.py
@@ -496,7 +496,7 @@ def __init__(self, spatial_extent, **kwarg):
             self._spatial_ext = [float(i) for i in arrpoly]
 
         # check for cross dateline keyword submission
-        if "xdateline" in kwarg.keys():
+        if "xdateline" in kwarg:
             self._xdateln = kwarg["xdateline"]
             assert self._xdateln in [
                 True,
@@ -542,10 +542,7 @@ def extent_as_gdf(self):
         """
 
         # TODO: test this
-        if hasattr(self, "_xdateln"):
-            xdateln = self._xdateln
-        else:
-            xdateln = None
+        xdateln = self._xdateln if hasattr(self, "_xdateln") else None
 
         if not hasattr(self, "_gdf_spat"):
             if self._geom_file is not None:

diff --git a/icepyx/core/variables.py b/icepyx/core/variables.py
@@ -84,10 +84,7 @@ def __init__(
             self._path = val.check_s3bucket(path)
 
             # Set up auth
-            if self._path.startswith("s3"):
-                auth = self.auth
-            else:
-                auth = None
+            auth = self.auth if self._path.startswith("s3") else None
             # Read the product and version from the file
             self._product = is2ref.extract_product(self._path, auth=auth)
             self._version = is2ref.extract_version(self._path, auth=auth)
@@ -111,11 +108,7 @@ def __init__(
 
     @property
     def path(self):
-        if self._path:
-            path = self._path
-        else:
-            path = None
-        return path
+        return self._path if self._path else None
 
     @property
     def product(self):
@@ -271,7 +264,7 @@ def parse_var_list(varlist, tiered=True, tiered_vars=False):
         for vn in varlist:
             vpath, vkey = os.path.split(vn)
             # print('path '+ vpath + ', key '+vkey)
-            if vkey not in vgrp.keys():
+            if vkey not in vgrp:
                 vgrp[vkey] = [vn]
             else:
                 vgrp[vkey].append(vn)
@@ -321,7 +314,7 @@ def _check_valid_lists(
         # check if the list of variables, if specified, are available in the product
         if var_list is not None:
             for var_id in var_list:
-                if var_id not in vgrp.keys():
+                if var_id not in vgrp:
                     err_msg_varid = "Invalid variable name: " + var_id + ". "
                     err_msg_varid = err_msg_varid + "Please select from this list: "
                     err_msg_varid = err_msg_varid + ", ".join(vgrp.keys())
@@ -514,9 +507,9 @@ def append(self, defaults=False, var_list=None, beam_list=None, keyword_list=Non
             )
 
         # update the data object variables
-        for vkey in final_vars.keys():
+        for vkey in final_vars:
             # add all matching keys and paths for new variables
-            if vkey not in self.wanted.keys():
+            if vkey not in self.wanted:
                 self.wanted[vkey] = final_vars[vkey]
             else:
                 for vpath in final_vars[vkey]:

diff --git a/icepyx/quest/dataset_scripts/__init__.py b/icepyx/quest/dataset_scripts/__init__.py
@@ -1 +1 @@
-from .dataset import *
+from .dataset import *  # noqa: F403