Repository: podaac/l2ss-py (language: python)

Issue:
Bump urllib3 from 1.26.16 to 1.26.17
Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.16 to 1.26.17.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/urllib3/urllib3/releases">urllib3's releases</a>.</em></p>
<blockquote>
<h2>1.26.17</h2>
<ul>
<li>Added the <code>Cookie</code> header to the list of headers to strip from requests when redirecting to a different host. As before, different headers can be set via <code>Retry.remove_headers_on_redirect</code>. (GHSA-v845-jxx5-vc9f)</li>
</ul>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/urllib3/urllib3/blob/main/CHANGES.rst">urllib3's changelog</a>.</em></p>
<blockquote>
<h1>1.26.17 (2023-10-02)</h1>
<ul>
<li>Added the <code>Cookie</code> header to the list of headers to strip from requests when redirecting to a different host. As before, different headers can be set via <code>Retry.remove_headers_on_redirect</code>. (<code>[#3139](https://github.com/urllib3/urllib3/issues/3139) &lt;https://github.com/urllib3/urllib3/pull/3139&gt;</code>_)</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/urllib3/urllib3/commit/c9016bf464751a02b7e46f8b86504f47d4238784"><code>c9016bf</code></a> Release 1.26.17</li>
<li><a href="https://github.com/urllib3/urllib3/commit/01220354d389cd05474713f8c982d05c9b17aafb"><code>0122035</code></a> Backport GHSA-v845-jxx5-vc9f (<a href="https://redirect.github.com/urllib3/urllib3/issues/3139">#3139</a>)</li>
<li><a href="https://github.com/urllib3/urllib3/commit/e63989f97d206e839ab9170c8a76e3e097cc60e8"><code>e63989f</code></a> Fix installing <code>brotli</code> extra on Python 2.7</li>
<li><a href="https://github.com/urllib3/urllib3/commit/2e7a24d08713a0131f0b3c7197889466d645cc49"><code>2e7a24d</code></a> [1.26] Configure OS for RTD to fix building docs</li>
<li><a href="https://github.com/urllib3/urllib3/commit/57181d6ea910ac7cb2ff83345d9e5e0eb816a0d0"><code>57181d6</code></a> [1.26] Improve error message when calling urllib3.request() (<a href="https://redirect.github.com/urllib3/urllib3/issues/3058">#3058</a>)</li>
<li><a href="https://github.com/urllib3/urllib3/commit/3c0148048a523325819377b23fc67f8d46afc3aa"><code>3c01480</code></a> [1.26] Run coverage even with failed jobs</li>
<li>See full diff in <a href="https://github.com/urllib3/urllib3/compare/1.26.16...1.26.17">compare view</a></li>
</ul>
</details>
<br />


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[//]: # (dependabot-automerge-start)
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---

<details>
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You can disable automated security fix PRs for this repo from the [Security Alerts page](https://github.com/podaac/l2ss-py/network/alerts).

</details>


Discussion / hints:

Fix patch:
diff --git a/.github/workflows/build-pipeline.yml b/.github/workflows/build-pipeline.yml
index fe0f3790..7ca4903f 100644
--- a/.github/workflows/build-pipeline.yml
+++ b/.github/workflows/build-pipeline.yml
@@ -86,6 +86,29 @@ jobs:
         run: |
           poetry run pytest --junitxml=build/reports/pytest.xml --cov=podaac/ --cov-report=xml:build/reports/coverage.xml -m "not aws and not integration" tests/
       - name: SonarCloud Scan
+        id: sonarcloud
+        uses: sonarsource/sonarcloud-github-action@master
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        with:
+          args: >
+            -Dsonar.organization=${{ github.repository_owner }}
+            -Dsonar.projectKey=${{ github.repository_owner }}_l2ss-py
+            -Dsonar.python.coverage.reportPaths=build/reports/coverage.xml
+            -Dsonar.sources=podaac/
+            -Dsonar.tests=tests/
+            -Dsonar.projectName=l2ss-py
+            -Dsonar.projectVersion=${{ env.software_version }}
+            -Dsonar.python.version=3.8,3.9,3.10
+        continue-on-error: true
+      - name: Wait to retry sonarcloud scan
+        if: steps.sonarcloud.outcome == 'failure'
+        run: |
+          sleep 40
+      - name: SonarCloud Scan Retry
+        id: sonarcloud-retry
+        if: steps.sonarcloud.outcome == 'failure'
         uses: sonarsource/sonarcloud-github-action@master
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -142,17 +165,43 @@ jobs:
           git tag -a "${{ env.software_version }}" -m "Version ${{ env.software_version }}"
           git push origin "${{ env.software_version }}"
       - name: Publish UMM-S with new version
-        uses: podaac/cmr-umm-updater@0.3.0
+        id: publish-umm-s
+        uses: podaac/cmr-umm-updater@0.5.0
         if: |
           github.ref == 'refs/heads/main'    ||
           startsWith(github.ref, 'refs/heads/release')
         with:
-          umm-s-json: 'cmr/l2ss_cmr_umm_s.json'
+          umm-json: 'cmr/l2ss_cmr_umm_s.json'
+          provider: 'POCLOUD'
+          env: ${{ env.venue }}
+          version: ${{ env.software_version }}
+          timeout: 60
+          disable_removal: 'true'
+          umm_type: 'umm-s'
+          use_associations: 'false'        
+        env:
+          LAUNCHPAD_TOKEN_SIT: ${{secrets.LAUNCHPAD_TOKEN_SIT}}
+          LAUNCHPAD_TOKEN_UAT: ${{secrets.LAUNCHPAD_TOKEN_UAT}}
+          LAUNCHPAD_TOKEN_OPS: ${{secrets.LAUNCHPAD_TOKEN_OPS}}
+        continue-on-error: true
+      - name: Wait to retry publishing umm-s
+        if: steps.publish-umm-s.outcome == 'failure'
+        run: |
+          sleep 120
+      - name: Publish UMM-S with new version retry
+        id: publish-umm-s-retry
+        uses: podaac/cmr-umm-updater@0.5.0
+        if: |
+          steps.publish-umm-s.outcome == 'failure'
+        with:
+          umm-json: 'cmr/l2ss_cmr_umm_s.json'
           provider: 'POCLOUD'
           env: ${{ env.venue }}
           version: ${{ env.software_version }}
           timeout: 60
           disable_removal: 'true'
+          umm_type: 'umm-s'
+          use_associations: 'false'        
         env:
           LAUNCHPAD_TOKEN_SIT: ${{secrets.LAUNCHPAD_TOKEN_SIT}}
           LAUNCHPAD_TOKEN_UAT: ${{secrets.LAUNCHPAD_TOKEN_UAT}}
diff --git a/.github/workflows/release-created.yml b/.github/workflows/release-created.yml
index 8984185a..ccb1b139 100644
--- a/.github/workflows/release-created.yml
+++ b/.github/workflows/release-created.yml
@@ -21,7 +21,7 @@ jobs:
           ref: 'refs/heads/develop'
       - uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
       - name: Install Poetry
         uses: abatilo/actions-poetry@v2.0.0
         with:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index b7822525..7d4103ae 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,23 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Security
 
 
+## [2.6.0]
+### Added
+### Changed
+- [issue/182](https://github.com/podaac/l2ss-py/issues/182): Update code so doesn't remove '/' on attribute values.
+- [issue/178](https://github.com/podaac/l2ss-py/issues/178): Add function to make sure dimension in subset is same as original file
+- Update github action umm updater to 0.5.0
+- [issue/172](https://github.com/podaac/l2ss-py/issues/178): Fix shapefile subsetting by passing correct variable to subset function.
+### Deprecated 
+### Removed
+### Fixed
+- [issue/119](https://github.com/podaac/l2ss-py/issues/119): GPM variable dimensions are renamed from "phony_dim" to the dimension names in the variable attribute "DimensionNames"
+- [issue/184](https://github.com/podaac/l2ss-py/issues/184): boundary box argument at the command line is changed to allow decimal numbers (i.e., floats) for coordinates
+- [issue/189](https://github.com/podaac/l2ss-py/issues/189): Fix temporal subsetting for SWOT collections, use mask_and_scale args for opening granule file if we have an overflow in time fill value, use original dataset encoding when writing file.
+- [issue/194](https://github.com/podaac/l2ss-py/issues/194): Return coordinate variables if requested in a variable subset
+### Security
+
+
 ## [2.5.0]
 ### Added
 ### Changed
diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt
index 13b3f04a..8eb4d153 100644
--- a/cmr/ops_associations.txt
+++ b/cmr/ops_associations.txt
@@ -86,3 +86,5 @@ C2601584109-POCLOUD
 C2601583089-POCLOUD
 C2601581863-POCLOUD
 C2628598397-POCLOUD
+C2036882456-POCLOUD
+C2296989380-POCLOUD
diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt
index 50344829..040c0c16 100644
--- a/cmr/uat_associations.txt
+++ b/cmr/uat_associations.txt
@@ -89,3 +89,5 @@ C1256507990-POCLOUD
 C1256122852-POCLOUD
 C1256507989-POCLOUD
 C1238621112-POCLOUD
+C1238621111-POCLOUD
+C1238687282-POCLOUD
diff --git a/podaac/subsetter/dimension_cleanup.py b/podaac/subsetter/dimension_cleanup.py
index 9ea3ce5e..556d3dd0 100644
--- a/podaac/subsetter/dimension_cleanup.py
+++ b/podaac/subsetter/dimension_cleanup.py
@@ -14,6 +14,7 @@
 import collections
 
 import netCDF4 as nc
+import xarray as xr
 
 
 def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset:
@@ -88,3 +89,21 @@ def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset:
         new_dup_var[dup_var_name][:] = dup_var[:]
 
     return nc_dataset
+
+
+def sync_dims_inplace(original_dataset: xr.Dataset, new_dataset: xr.Dataset) -> None:
+    """
+    Synchronize dimensions of variables in the new dataset with the original dataset.
+
+    Parameters:
+    original_dataset (xr.Dataset): The original dataset.
+    new_dataset (xr.Dataset): The new dataset with possibly additional dimensions.
+    """
+
+    for variable_name in new_dataset.variables:
+        original_variable_dims = original_dataset[variable_name].dims
+        new_variable_dims = new_dataset[variable_name].dims
+
+        for new_dim in new_variable_dims:
+            if new_dim not in original_variable_dims:
+                new_dataset[variable_name] = new_dataset[variable_name].isel({new_dim: 0})
diff --git a/podaac/subsetter/gpm_cleanup.py b/podaac/subsetter/gpm_cleanup.py
new file mode 100644
index 00000000..19b6f8e2
--- /dev/null
+++ b/podaac/subsetter/gpm_cleanup.py
@@ -0,0 +1,65 @@
+"""
+Module designed for mapping the dimensions in GPM. Phony dimensions are changed
+to nscan, nbin, nfreq by using the DimensionNames variable attribute
+"""
+
+dim_dict = {}
+
+
+def change_var_dims(nc_dataset, variables=None):
+    """
+    Go through each variable and get the dimension names from attribute "DimensionNames
+    If the name is unique, add it as a dimension to the netCDF4 dataset. Then change the
+    dimensions to have the name in the DimensionName attribute rather than phony_dim
+    """
+    var_list = list(nc_dataset.variables.keys())
+    # loop through variable list to avoid netcdf4 runtime error
+    for var_name in var_list:
+        # GPM will always need to be cleaned up via netCDF
+        # generalizing coordinate variables in netCDF file to speed variable subsetting up
+        if variables:
+            if var_name not in variables and 'lat' not in var_name.lower() and 'lon' not in var_name.lower() and 'time' not in var_name.lower():
+                # delete the uneccesary variables
+                del nc_dataset.variables[var_name]
+                continue
+
+        var = nc_dataset.variables[var_name]
+        # get the DimensionName attribute from the variable
+        if 'DimensionNames' in var.ncattrs():
+            dim_list = var.getncattr('DimensionNames').split(',')
+            # create dimension map
+            for count, dim in enumerate(dim_list):
+                # get unique group for new dimension name
+                dim_prefix = var_name.split('__')[1]
+                # new dimension name
+                new_dim = '__'+dim_prefix+'__'+dim
+                length = var.shape[count]
+                # check if the dimension name created has already been created in the dataset
+                if new_dim not in dim_dict:
+                    # create the new dimension
+                    nc_dataset.createDimension(new_dim, length)
+                    dim_dict[new_dim] = length
+            # utilized from Dimension Cleanup module
+            attrs_contents = {}
+            new_mapped_var = {}
+            # if the variable has attributes, get the attributes to then be copied to the new variable
+            if len(var.ncattrs()) > 0:
+                for attrname in var.ncattrs():
+                    if attrname != '_FillValue':
+                        attrs_contents[attrname] = nc_dataset.variables[var_name].getncattr(attrname)
+
+                fill_value = var._FillValue  # pylint: disable=W0212
+                dim_tup = ('__'+dim_prefix+'__'+i for i in var.getncattr('DimensionNames').split(','))
+                # delete the old variable with phony_dim names
+                del nc_dataset.variables[var_name]
+
+                # create the new variable with dimension names
+                new_mapped_var[var_name] = nc_dataset.createVariable(var_name, str(var[:].dtype),
+                                                                     dim_tup, fill_value=fill_value)
+                for attr_name, contents in attrs_contents.items():
+                    new_mapped_var[var_name].setncattr(attr_name, contents)
+
+                # copy the data to the new variable with dimension names
+                new_mapped_var[var_name][:] = var[:]
+
+    return nc_dataset
diff --git a/podaac/subsetter/group_handling.py b/podaac/subsetter/group_handling.py
index f2e62f73..8fa78c76 100644
--- a/podaac/subsetter/group_handling.py
+++ b/podaac/subsetter/group_handling.py
@@ -93,7 +93,7 @@ def walk(group_node, path):
     return nc_dataset
 
 
-def recombine_grouped_datasets(datasets: List[xr.Dataset], output_file: str, start_date) -> None:  # pylint: disable=too-many-branches
+def recombine_grouped_datasets(datasets: List[xr.Dataset], output_file: str, start_date, time_vars) -> None:  # pylint: disable=too-many-branches
     """
     Given a list of xarray datasets, combine those datasets into a
     single netCDF4 Dataset and write to the disk. Each dataset has been
@@ -126,7 +126,7 @@ def recombine_grouped_datasets(datasets: List[xr.Dataset], output_file: str, sta
             dim_group.createDimension(new_dim_name, dataset.dims[dim_name])
 
         # Rename variables
-        _rename_variables(dataset, base_dataset, start_date)
+        _rename_variables(dataset, base_dataset, start_date, time_vars)
 
     # Remove group vars from base dataset
     for var_name in list(base_dataset.variables.keys()):
@@ -151,7 +151,7 @@ def _get_nested_group(dataset: nc.Dataset, group_path: str) -> nc.Group:
     return nested_group
 
 
-def _rename_variables(dataset: xr.Dataset, base_dataset: nc.Dataset, start_date) -> None:
+def _rename_variables(dataset: xr.Dataset, base_dataset: nc.Dataset, start_date, time_vars) -> None:
     for var_name in list(dataset.variables.keys()):
         new_var_name = var_name.split(GROUP_DELIM)[-1]
         var_group = _get_nested_group(base_dataset, var_name)
@@ -161,7 +161,7 @@ def _rename_variables(dataset: xr.Dataset, base_dataset: nc.Dataset, start_date)
                 dataset.variables[var_name].dtype, np.dtype(np.datetime64)
         ) or np.issubdtype(
             dataset.variables[var_name].dtype, np.dtype(np.timedelta64)
-        ):
+        ) and var_name in time_vars:  # check that time changes are done to a time variable
             if start_date:
                 dataset.variables[var_name].values = (dataset.variables[var_name].values - np.datetime64(start_date))/np.timedelta64(1, 's')
                 variable = dataset.variables[var_name]
@@ -241,6 +241,20 @@ def walk_h5py(data_new, group):
 
     walk_h5py(data_new, data_new.name)
 
+    # Get the instrument name from the file attributes
+
+    additional_file_attributes = data_new.get('__HDFEOS__ADDITIONAL__FILE_ATTRIBUTES')
+    instrument = ""
+
+    if additional_file_attributes:
+        instrument = additional_file_attributes.attrs['InstrumentName'].decode("utf-8")
+    if 'OMI' in instrument:
+        hdf_type = 'OMI'
+    elif 'MLS' in instrument:
+        hdf_type = 'MLS'
+    else:
+        hdf_type = None
+
     for del_group in del_group_list:
         del data_new[del_group]
 
@@ -251,4 +265,4 @@ def walk_h5py(data_new, group):
 
     nc_dataset = nc.Dataset(finputnc, mode='r')
 
-    return nc_dataset, has_groups
+    return nc_dataset, has_groups, hdf_type
diff --git a/podaac/subsetter/run_subsetter.py b/podaac/subsetter/run_subsetter.py
index d3a499f4..45f341ce 100644
--- a/podaac/subsetter/run_subsetter.py
+++ b/podaac/subsetter/run_subsetter.py
@@ -35,7 +35,7 @@ def parse_args(args: list) -> tuple:
     )
     parser.add_argument(
         '--bbox',
-        type=int,
+        type=float,
         default=[-180, -90, 180, 90],
         nargs=4,
         action='store',
diff --git a/podaac/subsetter/subset.py b/podaac/subsetter/subset.py
index 20a3d403..a71d7efd 100644
--- a/podaac/subsetter/subset.py
+++ b/podaac/subsetter/subset.py
@@ -24,7 +24,7 @@
 import operator
 import os
 from itertools import zip_longest
-from typing import List, Tuple, Union
+from typing import List, Optional, Tuple, Union
 import dateutil
 from dateutil import parser
 
@@ -41,6 +41,8 @@
 from shapely.geometry import Point
 from shapely.ops import transform
 
+from podaac.subsetter import gpm_cleanup as gc
+from podaac.subsetter import time_converting as tc
 from podaac.subsetter import dimension_cleanup as dc
 from podaac.subsetter import xarray_enhancements as xre
 from podaac.subsetter.group_handling import GROUP_DELIM, transform_grouped_dataset, recombine_grouped_datasets, \
@@ -532,7 +534,7 @@ def compute_time_variable_name(dataset: xr.Dataset, lat_var: xr.Variable) -> str
         var_name_time = var_name.strip(GROUP_DELIM).split(GROUP_DELIM)[-1]
         if len(dataset[var_name].squeeze().dims) == 0:
             continue
-        if 'time' == var_name_time.lower() and dataset[var_name].squeeze().dims[0] in lat_var.squeeze().dims:
+        if ('time' == var_name_time.lower() or 'timeMidScan' == var_name_time) and dataset[var_name].squeeze().dims[0] in lat_var.squeeze().dims:
             return var_name
 
     # then check if any variables have 'time' in the string if the above loop doesn't return anything
@@ -742,7 +744,7 @@ def build_cond(str_timestamp, compare):
     return temporal_cond
 
 
-def get_base_group_names(lats):  # pylint: disable=too-many-branches
+def get_base_group_names(lats: List[str]) -> Tuple[List[str], List[Union[int, str]]]:  # pylint: disable=too-many-branches
     """Latitude groups may be at different depths. This function gets the level
     number that makes each latitude group unique from the other latitude names"""
     unique_groups = []
@@ -754,7 +756,7 @@ def get_base_group_names(lats):  # pylint: disable=too-many-branches
     # put the groups in the same levels in the same list
     group_list_transpose = np.array(group_list).T.tolist()
 
-    diff_count = ['' for i in range(len(group_list))]
+    diff_count = ['' for _ in range(len(group_list))]
     group_count = 0
     # loop through each group level
     for my_list in group_list_transpose:
@@ -786,7 +788,7 @@ def subset_with_bbox(dataset: xr.Dataset,  # pylint: disable=too-many-branches
                      lat_var_names: list,
                      lon_var_names: list,
                      time_var_names: list,
-                     variables=None,
+                     variables: Optional[List[str]] = None,
                      bbox: np.ndarray = None,
                      cut: bool = True,
                      min_time: str = None,
@@ -804,6 +806,8 @@ def subset_with_bbox(dataset: xr.Dataset,  # pylint: disable=too-many-branches
         Name of the longitude variables in the given dataset
     time_var_names : list
         Name of the time variables in the given dataset
+    variables : list[str]
+        List of variables to include in the result
     bbox : np.array
         Spatial bounding box to subset Dataset with.
     cut : bool
@@ -834,13 +838,6 @@ def subset_with_bbox(dataset: xr.Dataset,  # pylint: disable=too-many-branches
     else:
         unique_groups = [f'{GROUP_DELIM}{GROUP_DELIM.join(x.strip(GROUP_DELIM).split(GROUP_DELIM)[:-1])}' for x in lat_var_names]
 
-    # get unique group names for latitude coordinates
-    diff_count = [-1]
-    if len(lat_var_names) > 1:
-        unique_groups, diff_count = get_base_group_names(lat_var_names)
-    else:
-        unique_groups = [f'{GROUP_DELIM}{GROUP_DELIM.join(x.strip(GROUP_DELIM).split(GROUP_DELIM)[:-1])}' for x in lat_var_names]
-
     datasets = []
     total_list = []  # don't include repeated variables
     for lat_var_name, lon_var_name, time_var_name, diffs in zip(  # pylint: disable=too-many-nested-blocks
@@ -851,6 +848,11 @@ def subset_with_bbox(dataset: xr.Dataset,  # pylint: disable=too-many-branches
 
             if diffs == -1:  # if the lat name is in the root group: take only the root group vars
                 group_vars = list(dataset.data_vars.keys())
+                # include the coordinate variables if user asks for
+                group_vars.extend([
+                        var for var in list(dataset.coords.keys())
+                        if var in variables and var not in group_vars
+                    ])
             else:
                 group_vars = [
                     var for var in dataset.data_vars.keys()
@@ -859,13 +861,20 @@ def subset_with_bbox(dataset: xr.Dataset,  # pylint: disable=too-many-branches
                 # include variables that aren't in a latitude group
                 if variables:
                     group_vars.extend([
-                        var for var in dataset.data_vars.keys()
-                        if var in variables and var not in group_vars and var not in total_list and not var.startswith(tuple(unique_groups))
+                        var for var in dataset.variables.keys()
+                        if (var in variables and
+                            var not in group_vars and
+                            var not in total_list and
+                            not var.startswith(tuple(unique_groups))
+                            )
                     ])
                 else:
                     group_vars.extend([
                         var for var in dataset.data_vars.keys()
-                        if var not in group_vars and var not in total_list and not var.startswith(tuple(unique_groups))
+                        if (var not in group_vars and
+                            var not in total_list and
+                            not var.startswith(tuple(unique_groups))
+                            )
                         ])
 
                 # group dimensions do not get carried over if unused by data variables (MLS nTotalTimes var)
@@ -1020,64 +1029,24 @@ def get_coordinate_variable_names(dataset: xr.Dataset,
     return lat_var_names, lon_var_names, time_var_names
 
 
-def convert_to_datetime(dataset: xr.Dataset, time_vars: list) -> Tuple[xr.Dataset, datetime.datetime]:
-    """
-    Converts the time variable to datetime if xarray doesn't decode times
-
-    Parameters
-    ----------
-    dataset : xr.Dataset
-    time_vars : list
-
-    Returns
-    -------
-    xr.Dataset
-    datetime.datetime
-    """
-
-    for var in time_vars:
-        start_date = datetime.datetime.strptime("1993-01-01T00:00:00.00", "%Y-%m-%dT%H:%M:%S.%f")
-
-        if np.issubdtype(dataset[var].dtype, np.dtype(float)) or np.issubdtype(dataset[var].dtype, np.float32):
-            # adjust the time values from the start date
-            if start_date:
-                dataset[var].values = [start_date + datetime.timedelta(seconds=i) for i in dataset[var].values]
-                continue
-
-            utc_var_name = compute_utc_name(dataset)
-            if utc_var_name:
-                start_seconds = dataset[var].values[0]
-                dataset[var].values = [datetime.datetime(i[0], i[1], i[2], hour=i[3], minute=i[4], second=i[5]) for i in dataset[utc_var_name].values]
-                start_date = dataset[var].values[0] - np.timedelta64(int(start_seconds), 's')
-                return dataset, start_date
-
-        else:
-            pass
-
-    return dataset, start_date
-
-
 def open_as_nc_dataset(filepath: str) -> Tuple[nc.Dataset, bool]:
     """Open netcdf file, and flatten groups if they exist."""
-    file_extension = filepath.split('.')[-1]
+    hdf_type = None
+    # Open dataset with netCDF4 first, so we can get group info
+    try:
+        nc_dataset = nc.Dataset(filepath, mode='r')
+        has_groups = bool(nc_dataset.groups)
 
-    if file_extension == 'he5':
-        nc_dataset, has_groups = h5file_transform(filepath)
-    else:
-        # Open dataset with netCDF4 first, so we can get group info
-        try:
-            nc_dataset = nc.Dataset(filepath, mode='r')
-            has_groups = bool(nc_dataset.groups)
+        # If dataset has groups, transform to work with xarray
+        if has_groups:
+            nc_dataset = transform_grouped_dataset(nc_dataset, filepath)
 
-            # If dataset has groups, transform to work with xarray
-            if has_groups:
-                nc_dataset = transform_grouped_dataset(nc_dataset, filepath)
-        except OSError:
-            nc_dataset, has_groups = h5file_transform(filepath)
+    except OSError:
+        nc_dataset, has_groups, hdf_type = h5file_transform(filepath)
 
     nc_dataset = dc.remove_duplicate_dims(nc_dataset)
 
-    return nc_dataset, has_groups, file_extension
+    return nc_dataset, has_groups, hdf_type
 
 
 def override_decode_cf_datetime() -> None:
@@ -1161,7 +1130,8 @@ def subset(file_to_subset: str, bbox: np.ndarray, output_file: str,
         than one value in the case where there are multiple groups and
         different coordinate variables for each group.
     """
-    nc_dataset, has_groups, file_extension = open_as_nc_dataset(file_to_subset)
+    file_extension = os.path.splitext(file_to_subset)[1]
+    nc_dataset, has_groups, hdf_type = open_as_nc_dataset(file_to_subset)
 
     override_decode_cf_datetime()
 
@@ -1179,6 +1149,12 @@ def subset(file_to_subset: str, bbox: np.ndarray, output_file: str,
         lon_var_names = [var.replace('/', GROUP_DELIM) for var in lon_var_names]
         time_var_names = [var.replace('/', GROUP_DELIM) for var in time_var_names]
 
+    if '.HDF5' == file_extension:
+        # GPM files will have a timeMidScan time variable present
+        if '__FS__navigation__timeMidScan' in list(nc_dataset.variables.keys()):
+            gc.change_var_dims(nc_dataset, variables)
+            hdf_type = 'GPM'
+
     args = {
         'decode_coords': False,
         'mask_and_scale': False,
@@ -1193,19 +1169,33 @@ def subset(file_to_subset: str, bbox: np.ndarray, output_file: str,
 
     if min_time or max_time:
         args['decode_times'] = True
+        # check fill value and dtype, we know that this will cause an integer Overflow with xarray
+        if 'time' in nc_dataset.variables.keys():
+            try:
+                if nc_dataset['time'].getncattr('_FillValue') == nc.default_fillvals.get('f8') and \
+                 nc_dataset['time'].dtype == 'float64':
+                    args['mask_and_scale'] = True
+            except AttributeError:
+                pass
+
     with xr.open_dataset(
             xr.backends.NetCDF4DataStore(nc_dataset),
             **args
     ) as dataset:
+
+        original_dataset = dataset
+
         lat_var_names, lon_var_names, time_var_names = get_coordinate_variable_names(
             dataset=dataset,
             lat_var_names=lat_var_names,
             lon_var_names=lon_var_names,
             time_var_names=time_var_names
         )
+
         start_date = None
-        if file_extension == 'he5' and (min_time or max_time):
-            dataset, start_date = convert_to_datetime(dataset, time_var_names)
+        if hdf_type and (min_time or max_time):
+            dataset, start_date = tc.convert_to_datetime(dataset, time_var_names, hdf_type)
+
         chunks = calculate_chunks(dataset)
         if chunks:
             dataset = dataset.chunk(chunks)
@@ -1253,35 +1243,25 @@ def subset(file_to_subset: str, bbox: np.ndarray, output_file: str,
                     lon_var_names=lon_var_names
                 ))
             else:
-                encoding = {}
-                compression = {"zlib": True, "complevel": 5, "_FillValue": None}
-
-                if (min_time or max_time) and not all(
-                        dim_size == 1 for dim_size in dataset.dims.values()):
-                    encoding = {
-                        var_name: {
-                            'units': nc_dataset.variables[var_name].__dict__['units'],
-                            'zlib': True,
-                            "complevel": 5,
-                            "_FillValue": None
-                        } for var_name in time_var_names
-                        if 'units' in nc_dataset.variables[var_name].__dict__
-                    }
                 for var in dataset.data_vars:
-                    if var not in encoding:
-                        encoding[var] = compression
                     if dataset[var].dtype == 'S1' and isinstance(dataset[var].attrs.get('_FillValue'), bytes):
                         dataset[var].attrs['_FillValue'] = dataset[var].attrs['_FillValue'].decode('UTF-8')
 
+                    var_encoding = {
+                        "zlib": True,
+                        "complevel": 5,
+                        "_FillValue": original_dataset[var].encoding.get('_FillValue')
+                    }
+
                     data_var = dataset[var].copy()
-                    data_var.load().to_netcdf(output_file, 'a', encoding={var: encoding.get(var)})
+                    data_var.load().to_netcdf(output_file, 'a', encoding={var: var_encoding})
                     del data_var
 
                 with nc.Dataset(output_file, 'a') as dataset_attr:
                     dataset_attr.setncatts(dataset.attrs)
 
         if has_groups:
-            recombine_grouped_datasets(datasets, output_file, start_date)
+            recombine_grouped_datasets(datasets, output_file, start_date, time_var_names)
             # Check if the spatial bounds are all 'None'. This means the
             # subset result is empty.
             if any(bound is None for bound in spatial_bounds):
diff --git a/podaac/subsetter/subset_harmony.py b/podaac/subsetter/subset_harmony.py
index d120f1cd..7dfc84ef 100644
--- a/podaac/subsetter/subset_harmony.py
+++ b/podaac/subsetter/subset_harmony.py
@@ -136,7 +136,7 @@ def process_item(self, item: pystac.Item, source: harmony.message.Source) -> pys
                 harmony_bbox = message.subset.bbox
 
             if message.subset and message.subset.shape:
-                subset_params['shapefile_path'] = download(
+                subset_params['shapefile'] = download(
                     message.subset.shape.href,
                     temp_dir,
                     logger=self.logger,
diff --git a/podaac/subsetter/time_converting.py b/podaac/subsetter/time_converting.py
new file mode 100644
index 00000000..4332a176
--- /dev/null
+++ b/podaac/subsetter/time_converting.py
@@ -0,0 +1,61 @@
+"""
+Converts the time variable to datetime if xarray doesn't decode times
+
+Parameters
+----------
+dataset : xr.Dataset
+time_vars : list
+instrument_type: string
+
+Returns
+-------
+xr.Dataset
+datetime.datetime
+"""
+
+import datetime
+from typing import Tuple
+import xarray as xr
+import numpy as np
+from podaac.subsetter import subset
+
+
+def get_start_date(instrument_type):
+    """
+    returns the start date based on the instrument type
+    """
+    if instrument_type in ['OMI', 'MLS']:
+        start_date = datetime.datetime.strptime("1993-01-01T00:00:00.00", "%Y-%m-%dT%H:%M:%S.%f")
+    elif instrument_type in ['GPM']:
+        start_date = datetime.datetime.strptime("1980-01-06T00:00:00.00", "%Y-%m-%dT%H:%M:%S.%f")
+    else:
+        return None
+
+    return start_date
+
+
+def convert_to_datetime(dataset: xr.Dataset, time_vars: list, instrument_type: str) -> Tuple[xr.Dataset, datetime.datetime]:
+    """
+    Get the start date based on what the Instrument type is
+    Then convert the time variable from seconds since the start date to a datetime format
+    """
+    start_date = get_start_date(instrument_type)
+
+    for var in time_vars:
+        if np.issubdtype(dataset[var].dtype, np.dtype(float)) or np.issubdtype(dataset[var].dtype, np.float32):
+            # adjust the time values from the start date
+            if start_date:
+                dataset[var].values = [start_date + datetime.timedelta(seconds=i) for i in dataset[var].values]
+                continue
+            # if there isn't a start_date, get it from the UTC variable
+            utc_var_name = subset.compute_utc_name(dataset)
+            if utc_var_name:
+                start_seconds = dataset[var].values[0]
+                dataset[var].values = [datetime.datetime(i[0], i[1], i[2], hour=i[3], minute=i[4], second=i[5]) for i in dataset[utc_var_name].values]
+                start_date = dataset[var].values[0] - np.timedelta64(int(start_seconds), 's')
+                return dataset, start_date
+
+        else:
+            pass
+
+    return dataset, start_date
diff --git a/podaac/subsetter/xarray_enhancements.py b/podaac/subsetter/xarray_enhancements.py
index c9ebb319..5930b482 100644
--- a/podaac/subsetter/xarray_enhancements.py
+++ b/podaac/subsetter/xarray_enhancements.py
@@ -24,6 +24,7 @@
 
 import numpy as np
 import xarray as xr
+from podaac.subsetter import dimension_cleanup as dc
 
 
 def get_indexers_from_1d(cond: xr.Dataset) -> dict:
@@ -53,7 +54,7 @@ def get_indexers_from_1d(cond: xr.Dataset) -> dict:
 
 def get_indexers_from_nd(cond: xr.Dataset, cut: bool) -> dict:
     """
-    Get indexers from a dataset with more than 1 dimensions.
+    Get indexers from a dataset with more than one dimension.
 
     Parameters
     ----------
@@ -208,7 +209,6 @@ def where(dataset: xr.Dataset, cond: Union[xr.Dataset, xr.DataArray], cut: bool)
 
     indexed_cond = cond.isel(**indexers)
     indexed_ds = dataset.isel(**indexers)
-
     subset_vars, non_subset_vars = get_variables_with_indexers(dataset, indexers)
 
     # dataset with variables that need to be subsetted
@@ -276,4 +276,5 @@ def where(dataset: xr.Dataset, cond: Union[xr.Dataset, xr.DataArray], cut: bool)
                                                             str(original_type), dask='allowed',
                                                             keep_attrs=True)
 
+    dc.sync_dims_inplace(dataset, new_dataset)
     return new_dataset
diff --git a/poetry.lock b/poetry.lock
index 39786415..4d90c4cd 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -12,16 +12,28 @@ files = [
     {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
 ]
 
+[[package]]
+name = "annotated-types"
+version = "0.5.0"
+description = "Reusable constraint types to use with typing.Annotated"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "annotated_types-0.5.0-py3-none-any.whl", hash = "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"},
+    {file = "annotated_types-0.5.0.tar.gz", hash = "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802"},
+]
+
 [[package]]
 name = "astroid"
-version = "2.15.0"
+version = "2.15.8"
 description = "An abstract syntax tree for Python with inference support."
 category = "dev"
 optional = false
 python-versions = ">=3.7.2"
 files = [
-    {file = "astroid-2.15.0-py3-none-any.whl", hash = "sha256:e3e4d0ffc2d15d954065579689c36aac57a339a4679a679579af6401db4d3fdb"},
-    {file = "astroid-2.15.0.tar.gz", hash = "sha256:525f126d5dc1b8b0b6ee398b33159105615d92dc4a17f2cd064125d57f6186fa"},
+    {file = "astroid-2.15.8-py3-none-any.whl", hash = "sha256:1aa149fc5c6589e3d0ece885b4491acd80af4f087baafa3fb5203b113e68cd3c"},
+    {file = "astroid-2.15.8.tar.gz", hash = "sha256:6c107453dffee9055899705de3c9ead36e74119cee151e5a9aaf7f0b0e020a6a"},
 ]
 
 [package.dependencies]
@@ -34,54 +46,54 @@ wrapt = [
 
 [[package]]
 name = "attrs"
-version = "22.2.0"
+version = "23.1.0"
 description = "Classes Without Boilerplate"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "attrs-22.2.0-py3-none-any.whl", hash = "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836"},
-    {file = "attrs-22.2.0.tar.gz", hash = "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"},
+    {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
+    {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
 ]
 
 [package.extras]
-cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"]
-dev = ["attrs[docs,tests]"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"]
-tests = ["attrs[tests-no-zope]", "zope.interface"]
-tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy (>=0.971,<0.990)", "mypy (>=0.971,<0.990)", "pympler", "pympler", "pytest (>=4.3.0)", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-mypy-plugins", "pytest-xdist[psutil]", "pytest-xdist[psutil]"]
+cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
+dev = ["attrs[docs,tests]", "pre-commit"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
+tests = ["attrs[tests-no-zope]", "zope-interface"]
+tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "aws-sam-translator"
-version = "1.62.0"
+version = "1.76.0"
 description = "AWS SAM Translator is a library that transform SAM templates into AWS CloudFormation templates"
 category = "dev"
 optional = false
 python-versions = ">=3.7, <=4.0, !=4.0"
 files = [
-    {file = "aws-sam-translator-1.62.0.tar.gz", hash = "sha256:2db24633fbc76b8e6eb76adaf0c1001a0d749288af91d85e7d9007e3b05479fa"},
-    {file = "aws_sam_translator-1.62.0-py3-none-any.whl", hash = "sha256:5d198c8b4097b9210e1a44a64f55c4ee53b84f35d16ef1671b340242c41379cf"},
+    {file = "aws-sam-translator-1.76.0.tar.gz", hash = "sha256:6d0d68071071bd54c11ec69346a5a52db22cc316bfa2cb6f827a36a9348bbf00"},
+    {file = "aws_sam_translator-1.76.0-py3-none-any.whl", hash = "sha256:782ed1502d1a84a4912827da168edb133da9f8a5a7d5701cff7eede80ead1dca"},
 ]
 
 [package.dependencies]
 boto3 = ">=1.19.5,<2.0.0"
 jsonschema = ">=3.2,<5"
-pydantic = ">=1.8,<2.0"
+pydantic = ">=1.8,<3"
 typing-extensions = ">=4.4,<5"
 
 [package.extras]
-dev = ["black (==23.1.0)", "boto3 (>=1.23,<2)", "boto3-stubs[appconfig,serverlessrepo] (>=1.19.5,<2.0.0)", "coverage (>=5.3,<8)", "dateparser (>=1.1,<2.0)", "mypy (>=1.0.0,<1.1.0)", "parameterized (>=0.7,<1.0)", "pytest (>=6.2,<8)", "pytest-cov (>=2.10,<5)", "pytest-env (>=0.6,<1)", "pytest-rerunfailures (>=9.1,<12)", "pytest-xdist (>=2.5,<4)", "pyyaml (>=6.0,<7.0)", "requests (>=2.28,<3.0)", "ruamel.yaml (==0.17.21)", "ruff (==0.0.253)", "tenacity (>=8.0,<9.0)", "types-PyYAML (>=6.0,<7.0)", "types-jsonschema (>=3.2,<4.0)"]
+dev = ["black (==23.3.0)", "boto3 (>=1.23,<2)", "boto3-stubs[appconfig,serverlessrepo] (>=1.19.5,<2.0.0)", "coverage (>=5.3,<8)", "dateparser (>=1.1,<2.0)", "importlib-metadata", "mypy (>=1.3.0,<1.4.0)", "parameterized (>=0.7,<1.0)", "pytest (>=6.2,<8)", "pytest-cov (>=2.10,<5)", "pytest-env (>=0.6,<1)", "pytest-rerunfailures (>=9.1,<12)", "pytest-xdist (>=2.5,<4)", "pyyaml (>=6.0,<7.0)", "requests (>=2.28,<3.0)", "ruamel.yaml (==0.17.21)", "ruff (==0.0.284)", "tenacity (>=8.0,<9.0)", "types-PyYAML (>=6.0,<7.0)", "types-jsonschema (>=3.2,<4.0)"]
 
 [[package]]
 name = "aws-xray-sdk"
-version = "2.11.0"
+version = "2.12.0"
 description = "The AWS X-Ray SDK for Python (the SDK) enables Python developers to record and emit information from within their applications to the AWS X-Ray service."
 category = "dev"
 optional = false
 python-versions = "*"
 files = [
-    {file = "aws-xray-sdk-2.11.0.tar.gz", hash = "sha256:78835fc841f03e550858f18a9973eab8618f47f22d2f59edf130578fa545a867"},
-    {file = "aws_xray_sdk-2.11.0-py2.py3-none-any.whl", hash = "sha256:693fa3a4c790e131fe1e20814ede415a9eeeab5c3b7c868686d3e3c696b8524d"},
+    {file = "aws-xray-sdk-2.12.0.tar.gz", hash = "sha256:295afc237073a80956d7d4f27c31830edcb9a8ccca9ef8aa44990badef15e5b7"},
+    {file = "aws_xray_sdk-2.12.0-py2.py3-none-any.whl", hash = "sha256:30886e23cc2daadc1c06a76f25b071205e84848419d1ddf097b62a565e156542"},
 ]
 
 [package.dependencies]
@@ -90,39 +102,41 @@ wrapt = "*"
 
 [[package]]
 name = "babel"
-version = "2.12.1"
+version = "2.13.0"
 description = "Internationalization utilities"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"},
-    {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"},
+    {file = "Babel-2.13.0-py3-none-any.whl", hash = "sha256:fbfcae1575ff78e26c7449136f1abbefc3c13ce542eeb13d43d50d8b047216ec"},
+    {file = "Babel-2.13.0.tar.gz", hash = "sha256:04c3e2d28d2b7681644508f836be388ae49e0cfe91465095340395b60d00f210"},
 ]
 
-[package.dependencies]
-pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 
 [[package]]
 name = "bokeh"
-version = "2.4.3"
+version = "3.2.2"
 description = "Interactive plots and applications in the browser from Python"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
+contourpy = ">=1"
 Jinja2 = ">=2.9"
-numpy = ">=1.11.3"
+numpy = ">=1.16"
 packaging = ">=16.8"
+pandas = ">=1.2"
 pillow = ">=7.1.0"
 PyYAML = ">=3.10"
 tornado = ">=5.1"
-typing-extensions = ">=3.10.0"
+xyzservices = ">=2021.09.1"
 
 [[package]]
 name = "boto"
@@ -138,34 +152,34 @@ files = [
 
 [[package]]
 name = "boto3"
-version = "1.26.95"
+version = "1.28.58"
 description = "The AWS SDK for Python"
 category = "main"
 optional = false
 python-versions = ">= 3.7"
 files = [
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 ]
 
 [package.dependencies]
-botocore = ">=1.29.95,<1.30.0"
+botocore = ">=1.31.58,<1.32.0"
 jmespath = ">=0.7.1,<2.0.0"
-s3transfer = ">=0.6.0,<0.7.0"
+s3transfer = ">=0.7.0,<0.8.0"
 
 [package.extras]
 crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "botocore"
-version = "1.29.95"
+version = "1.31.58"
 description = "Low-level, data-driven core of boto 3."
 category = "main"
 optional = false
 python-versions = ">= 3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -174,110 +188,98 @@ python-dateutil = ">=2.1,<3.0.0"
 urllib3 = ">=1.25.4,<1.27"
 
 [package.extras]
-crt = ["awscrt (==0.16.9)"]
+crt = ["awscrt (==0.16.26)"]
 
 [[package]]
 name = "certifi"
-version = "2022.12.7"
+version = "2023.7.22"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
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 ]
 
 [[package]]
 name = "cf-xarray"
-version = "0.8.0"
+version = "0.8.4"
 description = "A convenience wrapper for using CF attributes on xarray objects"
 category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 xarray = "*"
 
 [package.extras]
-all = ["matplotlib", "pint", "regex", "rich", "shapely"]
+all = ["matplotlib", "pint", "pooch", "regex", "rich", "shapely"]
 
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 [package.dependencies]
@@ -285,25 +287,27 @@ pycparser = "*"
 
 [[package]]
 name = "cfn-lint"
-version = "0.75.1"
+version = "0.80.4"
 description = "Checks CloudFormation templates for practices and behaviour that could potentially be improved"
 category = "dev"
 optional = false
 python-versions = ">=3.7, <=4.0, !=4.0"
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 ]
 
 [package.dependencies]
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+aws-sam-translator = ">=1.73.0"
 jschema-to-python = ">=1.2.3,<1.3.0"
 jsonpatch = "*"
 jsonschema = ">=3.0,<5"
 junit-xml = ">=1.9,<2.0"
 networkx = ">=2.4,<4"
 pyyaml = ">5.4"
+regex = ">=2021.7.1"
 sarif-om = ">=1.0.4,<1.1.0"
+sympy = ">=1.0.0"
 
 [[package]]
 name = "cftime"
@@ -341,99 +345,114 @@ numpy = ">1.13.3"
 
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-version = "3.1.0"
+version = "3.3.0"
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 category = "main"
 optional = false
 python-versions = ">=3.7.0"
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 [package.dependencies]
@@ -568,31 +723,35 @@ toml = ["tomli"]
 
 [[package]]
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 category = "dev"
 optional = false
 python-versions = ">=3.7"
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 ]
 
 [package.dependencies]
@@ -610,39 +769,40 @@ test-randomorder = ["pytest-randomly"]
 
 [[package]]
 name = "dask"
-version = "2023.3.1"
+version = "2023.9.3"
 description = "Parallel PyData with Task Scheduling"
 category = "main"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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-    {file = "dask-2023.3.1.tar.gz", hash = "sha256:62d334012d7cd814186931ea83ebf1a6231c2af4260ad204dc78080a55947c17"},
+    {file = "dask-2023.9.3-py3-none-any.whl", hash = "sha256:2e6c5de0dfce114ca9c0bb2b79d72d3a9e1499bf25cfef477659179614df5692"},
+    {file = "dask-2023.9.3.tar.gz", hash = "sha256:712090788a7822d538cf8f43f5afc887eebe7471bc46cc331424e1cfa248764c"},
 ]
 
 [package.dependencies]
-bokeh = {version = ">=2.4.2,<3", optional = true, markers = "extra == \"complete\""}
-click = ">=7.0"
-cloudpickle = ">=1.1.1"
-distributed = {version = "2023.3.1", optional = true, markers = "extra == \"complete\""}
-fsspec = ">=0.6.0"
-jinja2 = {version = ">=2.10.3", optional = true, markers = "extra == \"complete\""}
+bokeh = {version = ">=2.4.2", optional = true, markers = "extra == \"diagnostics\""}
+click = ">=8.0"
+cloudpickle = ">=1.5.0"
+distributed = {version = "2023.9.3", optional = true, markers = "extra == \"distributed\""}
+fsspec = ">=2021.09.0"
+importlib-metadata = ">=4.13.0"
+jinja2 = {version = ">=2.10.3", optional = true, markers = "extra == \"diagnostics\""}
 lz4 = {version = ">=4.3.2", optional = true, markers = "extra == \"complete\""}
-numpy = {version = ">=1.21", optional = true, markers = "extra == \"complete\""}
+numpy = {version = ">=1.21", optional = true, markers = "extra == \"array\""}
 packaging = ">=20.0"
-pandas = {version = ">=1.3", optional = true, markers = "extra == \"complete\""}
+pandas = {version = ">=1.3", optional = true, markers = "extra == \"dataframe\""}
 partd = ">=1.2.0"
 pyarrow = {version = ">=7.0", optional = true, markers = "extra == \"complete\""}
 pyyaml = ">=5.3.1"
-toolz = ">=0.8.2"
+toolz = ">=0.10.0"
 
 [package.extras]
 array = ["numpy (>=1.21)"]
-complete = ["bokeh (>=2.4.2,<3)", "distributed (==2023.3.1)", "jinja2 (>=2.10.3)", "lz4 (>=4.3.2)", "numpy (>=1.21)", "pandas (>=1.3)", "pyarrow (>=7.0)"]
-dataframe = ["numpy (>=1.21)", "pandas (>=1.3)"]
-diagnostics = ["bokeh (>=2.4.2,<3)", "jinja2 (>=2.10.3)"]
-distributed = ["distributed (==2023.3.1)"]
-test = ["pandas[test]", "pre-commit", "pytest", "pytest-rerunfailures", "pytest-xdist"]
+complete = ["dask[array,dataframe,diagnostics,distributed]", "lz4 (>=4.3.2)", "pyarrow (>=7.0)"]
+dataframe = ["dask[array]", "pandas (>=1.3)"]
+diagnostics = ["bokeh (>=2.4.2)", "jinja2 (>=2.10.3)"]
+distributed = ["distributed (==2023.9.3)"]
+test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-rerunfailures", "pytest-timeout", "pytest-xdist"]
 
 [[package]]
 name = "deprecation"
@@ -661,14 +821,14 @@ packaging = "*"
 
 [[package]]
 name = "dill"
-version = "0.3.6"
-description = "serialize all of python"
+version = "0.3.7"
+description = "serialize all of Python"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -676,43 +836,43 @@ graph = ["objgraph (>=1.7.2)"]
 
 [[package]]
 name = "distributed"
-version = "2023.3.1"
+version = "2023.9.3"
 description = "Distributed scheduler for Dask"
 category = "main"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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+    {file = "distributed-2023.9.3.tar.gz", hash = "sha256:1161efaf7aa520fd0653ec48ceb59d3bc7d8931be392cf8bc7b89079739243e5"},
 ]
 
 [package.dependencies]
 click = ">=8.0"
 cloudpickle = ">=1.5.0"
-dask = "2023.3.1"
+dask = "2023.9.3"
 jinja2 = ">=2.10.3"
 locket = ">=1.0.0"
 msgpack = ">=1.0.0"
 packaging = ">=20.0"
-psutil = ">=5.7.0"
+psutil = ">=5.7.2"
 pyyaml = ">=5.3.1"
 sortedcontainers = ">=2.0.5"
 tblib = ">=1.6.0"
 toolz = ">=0.10.0"
-tornado = ">=6.0.3"
+tornado = ">=6.0.4"
 urllib3 = ">=1.24.3"
-zict = ">=2.1.0"
+zict = ">=3.0.0"
 
 [[package]]
 name = "docker"
-version = "6.0.1"
+version = "6.1.3"
 description = "A Python library for the Docker Engine API."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -758,14 +918,14 @@ gmpy2 = ["gmpy2"]
 
 [[package]]
 name = "exceptiongroup"
-version = "1.1.1"
+version = "1.1.3"
 description = "Backport of PEP 654 (exception groups)"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "exceptiongroup-1.1.3.tar.gz", hash = "sha256:097acd85d473d75af5bb98e41b61ff7fe35efe6675e4f9370ec6ec5126d160e9"},
 ]
 
 [package.extras]
@@ -773,28 +933,32 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "fiona"
-version = "1.9.2"
+version = "1.9.4.post1"
 description = "Fiona reads and writes spatial data files"
 category = "main"
 optional = false
 python-versions = ">=3.7"
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 ]
 
 [package.dependencies]
@@ -803,8 +967,7 @@ certifi = "*"
 click = ">=8.0,<9.0"
 click-plugins = ">=1.0"
 cligj = ">=0.5"
-importlib-metadata = {version = "*", markers = "python_version < \"3.10\""}
-munch = ">=2.3.2"
+six = "*"
 
 [package.extras]
 all = ["Fiona[calc,s3,test]"]
@@ -831,14 +994,14 @@ pyflakes = ">=2.3.0,<2.4.0"
 
 [[package]]
 name = "fsspec"
-version = "2023.3.0"
+version = "2023.9.2"
 description = "File-system specification"
 category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -846,7 +1009,9 @@ abfs = ["adlfs"]
 adl = ["adlfs"]
 arrow = ["pyarrow (>=1)"]
 dask = ["dask", "distributed"]
+devel = ["pytest", "pytest-cov"]
 dropbox = ["dropbox", "dropboxdrivefs", "requests"]
+full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "dask", "distributed", "dropbox", "dropboxdrivefs", "fusepy", "gcsfs", "libarchive-c", "ocifs", "panel", "paramiko", "pyarrow (>=1)", "pygit2", "requests", "s3fs", "smbprotocol", "tqdm"]
 fuse = ["fusepy"]
 gcs = ["gcsfs"]
 git = ["pygit2"]
@@ -883,52 +1048,48 @@ shapely = ">=1.6"
 
 [[package]]
 name = "h5py"
-version = "3.8.0"
+version = "3.9.0"
 description = "Read and write HDF5 files from Python"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
-numpy = ">=1.14.5"
+numpy = ">=1.17.3"
 
 [[package]]
 name = "harmony-service-lib"
-version = "1.0.22"
+version = "1.0.23"
 description = "A library for Python-based Harmony services to parse incoming messages, fetch data, stage data, and call back to Harmony"
 category = "main"
 optional = true
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -940,18 +1101,6 @@ python-json-logger = ">=2.0.1,<2.1.0"
 requests = ">=2.24,<3.0"
 urllib3 = ">=1.26.9,<1.27.0"
 
-[[package]]
-name = "heapdict"
-version = "1.0.1"
-description = "a heap with decrease-key and increase-key operations"
-category = "main"
-optional = false
-python-versions = "*"
-files = [
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-]
-
 [[package]]
 name = "idna"
 version = "2.8"
@@ -1086,14 +1235,14 @@ files = [
 
 [[package]]
 name = "jsonpatch"
-version = "1.32"
+version = "1.33"
 description = "Apply JSON-Patches (RFC 6902)"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
 files = [
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 ]
 
 [package.dependencies]
@@ -1101,14 +1250,14 @@ jsonpointer = ">=1.9"
 
 [[package]]
 name = "jsonpickle"
-version = "3.0.1"
+version = "3.0.2"
 description = "Python library for serializing any arbitrary object graph into JSON"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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-    {file = "jsonpickle-3.0.1.tar.gz", hash = "sha256:032538804795e73b94ead410800ac387fdb6de98f8882ac957fcd247e3a85200"},
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 ]
 
 [package.extras]
@@ -1118,14 +1267,14 @@ testing-libs = ["simplejson", "ujson"]
 
 [[package]]
 name = "jsonpointer"
-version = "2.3"
+version = "2.4"
 description = "Identify specific nodes in a JSON document (RFC 6901)"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
 files = [
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+    {file = "jsonpointer-2.4.tar.gz", hash = "sha256:585cee82b70211fa9e6043b7bb89db6e1aa49524340dde8ad6b63206ea689d88"},
 ]
 
 [[package]]
@@ -1302,62 +1451,62 @@ mistune = "0.8.4"
 
 [[package]]
 name = "markupsafe"
-version = "2.1.2"
+version = "2.1.3"
 description = "Safely add untrusted strings to HTML/XML markup."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 server = ["flask"]
 
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 [package.extras]
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 ]
 
 [[package]]
@@ -2420,21 +2805,21 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "responses"
-version = "0.23.1"
+version = "0.23.3"
 description = "A utility library for mocking out the `requests` Python library."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
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-requests = ">=2.22.0,<3.0"
+requests = ">=2.30.0,<3.0"
 types-PyYAML = "*"
-urllib3 = ">=1.25.10"
+urllib3 = ">=1.25.10,<3.0"
 
 [package.extras]
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@@ -2456,14 +2841,14 @@ pyasn1 = ">=0.1.3"
 
 [[package]]
 name = "s3transfer"
-version = "0.6.0"
+version = "0.7.0"
 description = "An Amazon S3 Transfer Manager"
 category = "main"
 optional = false
 python-versions = ">= 3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -2490,20 +2875,20 @@ pbr = "*"
 
 [[package]]
 name = "setuptools"
-version = "67.6.0"
+version = "68.2.2"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
-testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.1)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
 name = "shapely"
@@ -2616,7 +3001,6 @@ babel = ">=1.3"
 colorama = {version = ">=0.3.5", markers = "sys_platform == \"win32\""}
 docutils = ">=0.14,<0.18"
 imagesize = "*"
-importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
 Jinja2 = ">=2.3"
 packaging = "*"
 Pygments = ">=2.0"
@@ -2767,16 +3151,31 @@ ecdsa = ">=0.13"
 [package.extras]
 dev = ["twine", "wheel", "yapf"]
 
+[[package]]
+name = "sympy"
+version = "1.12"
+description = "Computer algebra system (CAS) in Python"
+category = "dev"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "sympy-1.12-py3-none-any.whl", hash = "sha256:c3588cd4295d0c0f603d0f2ae780587e64e2efeedb3521e46b9bb1d08d184fa5"},
+    {file = "sympy-1.12.tar.gz", hash = "sha256:ebf595c8dac3e0fdc4152c51878b498396ec7f30e7a914d6071e674d49420fb8"},
+]
+
+[package.dependencies]
+mpmath = ">=0.19"
+
 [[package]]
 name = "tblib"
-version = "1.7.0"
+version = "2.0.0"
 description = "Traceback serialization library."
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.7"
 files = [
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-    {file = "tblib-1.7.0.tar.gz", hash = "sha256:059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c"},
+    {file = "tblib-2.0.0-py3-none-any.whl", hash = "sha256:9100bfa016b047d5b980d66e7efed952fbd20bd85b56110aaf473cb97d18709a"},
+    {file = "tblib-2.0.0.tar.gz", hash = "sha256:a6df30f272c08bf8be66e0775fad862005d950a6b8449b94f7c788731d70ecd7"},
 ]
 
 [[package]]
@@ -2793,14 +3192,14 @@ files = [
 
 [[package]]
 name = "tomlkit"
-version = "0.11.6"
+version = "0.12.1"
 description = "Style preserving TOML library"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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-    {file = "tomlkit-0.11.6.tar.gz", hash = "sha256:71b952e5721688937fb02cf9d354dbcf0785066149d2855e44531ebdd2b65d73"},
+    {file = "tomlkit-0.12.1-py3-none-any.whl", hash = "sha256:712cbd236609acc6a3e2e97253dfc52d4c2082982a88f61b640ecf0817eab899"},
+    {file = "tomlkit-0.12.1.tar.gz", hash = "sha256:38e1ff8edb991273ec9f6181244a6a391ac30e9f5098e7535640ea6be97a7c86"},
 ]
 
 [[package]]
@@ -2817,100 +3216,112 @@ files = [
 
 [[package]]
 name = "tornado"
-version = "6.3.2"
+version = "6.3.3"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
 category = "main"
 optional = false
 python-versions = ">= 3.8"
 files = [
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+    {file = "tornado-6.3.3-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:71a8db65160a3c55d61839b7302a9a400074c9c753040455494e2af74e2501f2"},
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+    {file = "tornado-6.3.3-cp38-abi3-musllinux_1_1_x86_64.whl", hash = "sha256:9dc4444c0defcd3929d5c1eb5706cbe1b116e762ff3e0deca8b715d14bf6ec17"},
+    {file = "tornado-6.3.3-cp38-abi3-win32.whl", hash = "sha256:65ceca9500383fbdf33a98c0087cb975b2ef3bfb874cb35b8de8740cf7f41bd3"},
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+    {file = "tornado-6.3.3.tar.gz", hash = "sha256:e7d8db41c0181c80d76c982aacc442c0783a2c54d6400fe028954201a2e032fe"},
 ]
 
 [[package]]
 name = "types-pyyaml"
-version = "6.0.12.8"
+version = "6.0.12.12"
 description = "Typing stubs for PyYAML"
 category = "dev"
 optional = false
 python-versions = "*"
 files = [
-    {file = "types-PyYAML-6.0.12.8.tar.gz", hash = "sha256:19304869a89d49af00be681e7b267414df213f4eb89634c4495fa62e8f942b9f"},
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+    {file = "types_PyYAML-6.0.12.12-py3-none-any.whl", hash = "sha256:c05bc6c158facb0676674b7f11fe3960db4f389718e19e62bd2b84d6205cfd24"},
 ]
 
 [[package]]
 name = "typing-extensions"
-version = "4.5.0"
-description = "Backported and Experimental Type Hints for Python 3.7+"
+version = "4.8.0"
+description = "Backported and Experimental Type Hints for Python 3.8+"
+category = "dev"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "typing_extensions-4.8.0-py3-none-any.whl", hash = "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0"},
+    {file = "typing_extensions-4.8.0.tar.gz", hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"},
+]
+
+[[package]]
+name = "tzdata"
+version = "2023.3"
+description = "Provider of IANA time zone data"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=2"
 files = [
-    {file = "typing_extensions-4.5.0-py3-none-any.whl", hash = "sha256:fb33085c39dd998ac16d1431ebc293a8b3eedd00fd4a32de0ff79002c19511b4"},
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+    {file = "tzdata-2023.3-py2.py3-none-any.whl", hash = "sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda"},
+    {file = "tzdata-2023.3.tar.gz", hash = "sha256:11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a"},
 ]
 
 [[package]]
 name = "urllib3"
-version = "1.26.15"
+version = "1.26.17"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
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+    {file = "urllib3-1.26.17-py2.py3-none-any.whl", hash = "sha256:94a757d178c9be92ef5539b8840d48dc9cf1b2709c9d6b588232a055c524458b"},
+    {file = "urllib3-1.26.17.tar.gz", hash = "sha256:24d6a242c28d29af46c3fae832c36db3bbebcc533dd1bb549172cd739c82df21"},
 ]
 
 [package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
+brotli = ["brotli (==1.0.9)", "brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
 secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
 socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
 name = "websocket-client"
-version = "1.5.1"
+version = "1.6.3"
 description = "WebSocket client for Python with low level API options"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "websocket-client-1.5.1.tar.gz", hash = "sha256:3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40"},
-    {file = "websocket_client-1.5.1-py3-none-any.whl", hash = "sha256:cdf5877568b7e83aa7cf2244ab56a3213de587bbe0ce9d8b9600fc77b455d89e"},
+    {file = "websocket-client-1.6.3.tar.gz", hash = "sha256:3aad25d31284266bcfcfd1fd8a743f63282305a364b8d0948a43bd606acc652f"},
+    {file = "websocket_client-1.6.3-py3-none-any.whl", hash = "sha256:6cfc30d051ebabb73a5fa246efdcc14c8fbebbd0330f8984ac3bb6d9edd2ad03"},
 ]
 
 [package.extras]
-docs = ["Sphinx (>=3.4)", "sphinx-rtd-theme (>=0.5)"]
+docs = ["Sphinx (>=6.0)", "sphinx-rtd-theme (>=1.1.0)"]
 optional = ["python-socks", "wsaccel"]
 test = ["websockets"]
 
 [[package]]
 name = "werkzeug"
-version = "2.2.3"
+version = "3.0.0"
 description = "The comprehensive WSGI web application library."
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "Werkzeug-2.2.3-py3-none-any.whl", hash = "sha256:56433961bc1f12533306c624f3be5e744389ac61d722175d543e1751285da612"},
-    {file = "Werkzeug-2.2.3.tar.gz", hash = "sha256:2e1ccc9417d4da358b9de6f174e3ac094391ea1d4fbef2d667865d819dfd0afe"},
+    {file = "werkzeug-3.0.0-py3-none-any.whl", hash = "sha256:cbb2600f7eabe51dbc0502f58be0b3e1b96b893b05695ea2b35b43d4de2d9962"},
+    {file = "werkzeug-3.0.0.tar.gz", hash = "sha256:3ffff4dcc32db52ef3cc94dff3000a3c2846890f3a5a51800a27b909c5e770f0"},
 ]
 
 [package.dependencies]
 MarkupSafe = ">=2.1.1"
 
 [package.extras]
-watchdog = ["watchdog"]
+watchdog = ["watchdog (>=2.3)"]
 
 [[package]]
 name = "wrapt"
@@ -2999,27 +3410,26 @@ files = [
 
 [[package]]
 name = "xarray"
-version = "2023.1.0"
+version = "2023.9.0"
 description = "N-D labeled arrays and datasets in Python"
 category = "main"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "xarray-2023.1.0-py3-none-any.whl", hash = "sha256:7e530b1deafdd43e5c2b577d0944e6b528fbe88045fd849e49a8d11871ecd522"},
-    {file = "xarray-2023.1.0.tar.gz", hash = "sha256:7bee552751ff1b29dab8b7715726e5ecb56691ac54593cf4881dff41978ce0cd"},
+    {file = "xarray-2023.9.0-py3-none-any.whl", hash = "sha256:3fc4a558bd70968040a4e1cefc6ddb3f9a7a86ef6a48e67857156ffe655d3a66"},
+    {file = "xarray-2023.9.0.tar.gz", hash = "sha256:271955c05dc626dad37791a7807d920aaf9c64cac71d03b45ec7e402cc646603"},
 ]
 
 [package.dependencies]
 dask = {version = "*", extras = ["complete"], optional = true, markers = "extra == \"parallel\""}
-numpy = ">=1.20"
+numpy = ">=1.21"
 packaging = ">=21.3"
-pandas = ">=1.3"
+pandas = ">=1.4"
 
 [package.extras]
 accel = ["bottleneck", "flox", "numbagg", "scipy"]
-complete = ["bottleneck", "cfgrib", "cftime", "dask[complete]", "flox", "fsspec", "h5netcdf", "matplotlib", "nc-time-axis", "netCDF4", "numbagg", "pooch", "pydap", "rasterio", "scipy", "seaborn", "zarr"]
-docs = ["bottleneck", "cfgrib", "cftime", "dask[complete]", "flox", "fsspec", "h5netcdf", "ipykernel", "ipython", "jupyter-client", "matplotlib", "nbsphinx", "nc-time-axis", "netCDF4", "numbagg", "pooch", "pydap", "rasterio", "scanpydoc", "scipy", "seaborn", "sphinx-autosummary-accessors", "sphinx-rtd-theme", "zarr"]
-io = ["cfgrib", "cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap", "rasterio", "scipy", "zarr"]
+complete = ["xarray[accel,io,parallel,viz]"]
+io = ["cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap", "scipy", "zarr"]
 parallel = ["dask[complete]"]
 viz = ["matplotlib", "nc-time-axis", "seaborn"]
 
@@ -3035,41 +3445,50 @@ files = [
     {file = "xmltodict-0.13.0.tar.gz", hash = "sha256:341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56"},
 ]
 
+[[package]]
+name = "xyzservices"
+version = "2023.7.0"
+description = "Source of XYZ tiles providers"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "xyzservices-2023.7.0-py3-none-any.whl", hash = "sha256:88e9cbf22b31a2f9c1b242e2b18690f5c705f0e539c9bfd37a10399e1037731b"},
+    {file = "xyzservices-2023.7.0.tar.gz", hash = "sha256:0ec928742227d6f5d4367ea7b457fcfed943429f4de2949b5b02a82cdf5569d6"},
+]
+
 [[package]]
 name = "zict"
-version = "2.2.0"
+version = "3.0.0"
 description = "Mutable mapping tools"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "zict-2.2.0-py2.py3-none-any.whl", hash = "sha256:dabcc8c8b6833aa3b6602daad50f03da068322c1a90999ff78aed9eecc8fa92c"},
-    {file = "zict-2.2.0.tar.gz", hash = "sha256:d7366c2e2293314112dcf2432108428a67b927b00005619feefc310d12d833f3"},
+    {file = "zict-3.0.0-py2.py3-none-any.whl", hash = "sha256:5796e36bd0e0cc8cf0fbc1ace6a68912611c1dbd74750a3f3026b9b9d6a327ae"},
+    {file = "zict-3.0.0.tar.gz", hash = "sha256:e321e263b6a97aafc0790c3cfb3c04656b7066e6738c37fffcca95d803c9fba5"},
 ]
 
-[package.dependencies]
-heapdict = "*"
-
 [[package]]
 name = "zipp"
-version = "3.15.0"
+version = "3.17.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"},
-    {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"},
+    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
+    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
 
 [extras]
 harmony = ["harmony-service-lib", "pystac"]
 
 [metadata]
 lock-version = "2.0"
-python-versions = "^3.8"
-content-hash = "ad575d6c5a72d480f7deac708c218a7ba1ba17d9a21765207dbb890a7749f95f"
+python-versions = "^3.10"
+content-hash = "10a7857e4a505cb0af35901a6f1a9515e103375207edeaa67c8ad6f5f9478225"
diff --git a/pyproject.toml b/pyproject.toml
index a9b815d5..7d7b91fa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,7 +12,7 @@
 
 [tool.poetry]
 name = "l2ss-py"
-version = "2.5.0"
+version = "2.6.0rc16"
 description = "L2 Subsetter Service"
 authors = ["podaac-tva <podaac-tva@jpl.nasa.gov>"]
 license = "Apache-2.0"
@@ -27,7 +27,7 @@ packages = [
 ]
 
 [tool.poetry.dependencies]
-python = "^3.8"
+python = "^3.9"
 netCDF4 = "^1.5"
 xarray = {version = "*", extras = ["parallel"]}
 geopandas ="^0.10"


Test patch:
diff --git a/tests/data/GPM/GPM_test_file.HDF5 b/tests/data/GPM/GPM_test_file.HDF5
new file mode 100644
index 00000000..93491ed2
Binary files /dev/null and b/tests/data/GPM/GPM_test_file.HDF5 differ
diff --git a/tests/test_subset.py b/tests/test_subset.py
index 33c8ce39..b3f71ee4 100644
--- a/tests/test_subset.py
+++ b/tests/test_subset.py
@@ -51,6 +51,8 @@
 from podaac.subsetter.group_handling import GROUP_DELIM
 from podaac.subsetter.subset import SERVICE_NAME
 from podaac.subsetter import xarray_enhancements as xre
+from podaac.subsetter import gpm_cleanup as gc
+from podaac.subsetter import time_converting as tc
 # from podaac.subsetter import dimension_cleanup as dc
 
 
@@ -156,6 +158,24 @@ def test_subset_variables(test_file, data_dir, subset_output_dir, request):
                              decode_times=False,
                              decode_coords=False)
 
+
+    nc_in_ds = nc.Dataset(join(data_dir, test_file))
+    nc_out_ds = nc.Dataset(join(subset_output_dir, output_file))
+
+    time_var_name = None
+    try:
+        lat_var_name = subset.compute_coordinate_variable_names(in_ds)[0][0]
+        time_var_name = subset.compute_time_variable_name(in_ds, in_ds[lat_var_name])
+    except ValueError:
+        # unable to determine lon lat vars
+        pass
+
+    if time_var_name:
+        assert nc_in_ds[time_var_name].units == nc_out_ds[time_var_name].units
+
+    nc_in_ds.close()
+    nc_out_ds.close()
+
     for in_var, out_var in zip(in_ds.data_vars.items(), out_ds.data_vars.items()):
         # compare names
         assert in_var[0] == out_var[0]
@@ -1575,8 +1595,8 @@ def test_transform_h5py_dataset(data_dir, subset_output_dir):
                     entry_lst.append(entry_str + "/" + group_keys)
                 key_lst.append(entry_str + "/" + group_keys)
 
-    nc_dataset, _ = subset.h5file_transform(os.path.join(subset_output_dir, OMI_file_name))
-
+    nc_dataset, has_groups, hdf_type = subset.h5file_transform(os.path.join(subset_output_dir, OMI_file_name))
+    assert 'OMI' == hdf_type
     nc_vars_flattened = list(nc_dataset.variables.keys())
     for i, entry in enumerate(entry_lst):  # go through all the datasets in h5py file
         input_variable = '__' + entry.replace('/', '__')
@@ -1787,8 +1807,9 @@ def test_temporal_he5file_subset(data_dir, subset_output_dir):
         min_time = '2020-01-16T12:30:00Z'
         max_time = '2020-01-16T12:40:00Z'
 
-        nc_dataset, _ = subset.h5file_transform(os.path.join(subset_output_dir, OMI_copy_file))
-
+        nc_dataset, has_groups, hdf_type = subset.h5file_transform(os.path.join(subset_output_dir, OMI_copy_file))
+        assert has_groups == True
+        assert i[0] == hdf_type
         args = {
             'decode_coords': False,
             'mask_and_scale': False,
@@ -1810,12 +1831,15 @@ def test_temporal_he5file_subset(data_dir, subset_output_dir):
             )
             if 'BRO' in i:
                 assert any('utc' in x.lower() for x in time_var_names)
-
-            dataset, _ = subset.convert_to_datetime(dataset, time_var_names)
+            
+            dataset, _ = tc.convert_to_datetime(dataset, time_var_names, hdf_type)
             assert dataset[time_var_names[0]].dtype == 'datetime64[ns]'
 
 def test_MLS_levels(data_dir, subset_output_dir, request):
-    """"""
+    """
+    Test that the unique groups are determined before bounding box
+    subsetting
+    """
     mls_dir = join(data_dir, 'MLS')
     mls_file = 'MLS-Aura_L2GP-CO_v05-01-c01_2021d043.he5'
     mls_file_input = 'input' + mls_file
@@ -1953,7 +1977,7 @@ def test_get_time_OMI(data_dir, subset_output_dir):
     shutil.copyfile(os.path.join(data_dir, 'OMI', omi_file),
                     os.path.join(subset_output_dir, omi_file))
 
-    nc_dataset, _ = subset.h5file_transform(os.path.join(subset_output_dir, omi_file))
+    nc_dataset, has_groups, hdf_type = subset.h5file_transform(os.path.join(subset_output_dir, omi_file))
 
     args = {
         'decode_coords': False,
@@ -2117,7 +2141,7 @@ def test_tropomi_utc_time(data_dir, subset_output_dir, request):
     """Verify that the time UTC values are conserved in S5P files"""
     trop_dir = join(data_dir, 'tropomi')
     trop_file = 'S5P_OFFL_L2__CH4____20190319T110835_20190319T125006_07407_01_010202_20190325T125810_subset.nc4'
-    variable = ['/PRODUCT/time_utc']
+    variable = ['/PRODUCT/time_utc', '/PRODUCT/corner']
     bbox = np.array(((-180, 180), (-90, 90)))
     output_file = "{}_{}".format(request.node.name, trop_file)
     shutil.copyfile(
@@ -2137,6 +2161,8 @@ def test_tropomi_utc_time(data_dir, subset_output_dir, request):
     assert in_nc_dataset.groups['PRODUCT'].variables['time_utc'][:].squeeze()[0] ==\
                     out_nc_dataset.groups['PRODUCT'].variables['time_utc'][:].squeeze()[0]
 
+    assert out_nc_dataset.groups['PRODUCT'].variables['corner']
+
 def test_bad_time_unit(subset_output_dir):
     """TODO: give this function a description
     """
@@ -2208,3 +2234,25 @@ def test_get_unique_groups():
     
     assert expected_groups_single == unique_groups_single
     assert expected_diff_counts_single == diff_counts_single
+
+def test_gpm_dimension_map(data_dir, subset_output_dir, request):
+    """Test GPM files for dimension mapping and returns the expected netCDF
+       dataset without the phony dimensions"""
+    
+    gpm_dir = join(data_dir, 'GPM')
+    gpm_file = 'GPM_test_file.HDF5'
+    bbox = np.array(((-180, 180), (-90, 90)))
+    shutil.copyfile(
+        os.path.join(gpm_dir, gpm_file),
+        os.path.join(subset_output_dir, gpm_file)
+    )
+
+    nc_dataset, has_groups, file_extension = subset.open_as_nc_dataset(join(subset_output_dir, gpm_file))
+
+    nc_dataset = gc.change_var_dims(nc_dataset)
+
+    for var_name, var in nc_dataset.variables.items():
+        dims = list(var.dimensions)
+        
+        for dim in dims:
+            assert 'phony' not in dim