From d9fc7de244a1c3b452569c92784c6e47d33074b1 Mon Sep 17 00:00:00 2001
From: Daniel Kaufman <114174502+danielfromearth@users.noreply.github.com>
Date: Fri, 15 Nov 2024 11:16:17 -0500
Subject: [PATCH 01/37] Add gitleaks and update .pre-commit-config.yaml

---
 .pre-commit-config.yaml | 62 ++++++++++++++++++++++++-----------------
 1 file changed, 36 insertions(+), 26 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index f550c2e..8b37a02 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,46 +1,56 @@
----
 ci:
   autoupdate_schedule: "monthly" # Like dependabot
   autoupdate_commit_msg: "chore: update pre-commit hooks"
   autoupdate_branch: "develop"
   autofix_prs: false # Comment "pre-commit.ci autofix" on a PR to trigger
 
+default_language_version:
+  python: python3.10
+
 repos:
+  - repo: https://github.com/gitleaks/gitleaks
+    rev: v8.21.2
+    hooks:
+      - id: gitleaks
+
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
-      - id: trailing-whitespace
-        exclude: tests(/\w*)*/functional/t/trailing_whitespaces.py|tests/pyreverse/data/.*.html|doc/data/messages/t/trailing-whitespace/bad.py
+      # Validate format
+      - id: check-yaml
+      - id: check-toml
+      - id: check-json
+      # Check for common mistakes
+      - id: check-added-large-files
+      - id: check-case-conflict
+      # - id: check-illegal-windows-names # TODO: Enable in next release
+      - id: check-merge-conflict
+      - id: check-executables-have-shebangs
+      - id: check-shebang-scripts-are-executable
+      - id: check-symlinks
+      - id: check-vcs-permalinks
+      - id: destroyed-symlinks
+      - id: detect-private-key
       - id: end-of-file-fixer
-        exclude: |
-          (?x)^(
-            tests(/\w*)*/functional/m/missing/missing_final_newline.py|
-            tests/functional/t/trailing_newlines.py|
-            doc/data/messages/t/trailing-newlines/bad.py|
-          )$
+      - id: mixed-line-ending
+      - id: no-commit-to-branch # protects `main` by default
+      - id: debug-statements
+      - id: trailing-whitespace
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    # Ruff version.
-    rev: 'v0.7.0'
+    rev: v0.7.3
     hooks:
       - id: ruff
-        args: [ "--fix" ]
-
-  # https://github.com/python/black#version-control-integration
-  - repo: https://github.com/psf/black
-    rev: 24.10.0
-    hooks:
-      - id: black-jupyter
+        args: ["--fix", "--exit-non-zero-on-fix"]
+      - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.12.1
+    rev: v1.13.0
     hooks:
       - id: mypy
 
-  # Other Linters
-  - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.35.1
-    hooks:
-      - id: yamllint
-        args: ["-d {extends: relaxed, rules: {line-length: {max: 120}}}"]
-        stages: [commit, push]
+# TODO: Reconsider using the alexjs hook when there is a way to ignore particular warnings and/or files.
+#  - repo: "https://github.com/mfisher87/alexjs-pre-commit-mirror"
+#    rev: "v11.0.1"  # Use the sha / tag you prefer
+#    hooks:
+#      - id: "alex"

From 3434e0a6413923f8e6a951820a20f7e1c73f8c5d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 15 Nov 2024 16:47:30 +0000
Subject: [PATCH 02/37] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 concatenator/attribute_handling.py            | 10 +++--
 concatenator/dataset_and_group_handling.py    | 32 ++++++++++----
 concatenator/dimension_cleanup.py             | 35 +++++++++++-----
 concatenator/file_ops.py                      |  8 +++-
 concatenator/harmony/download_worker.py       | 16 +++++--
 concatenator/harmony/service_adapter.py       | 22 +++++++---
 concatenator/harmony/util.py                  |  6 ++-
 concatenator/run_stitchee.py                  |  5 ++-
 concatenator/stitchee.py                      | 19 ++++++---
 docs/tutorial_examples.ipynb                  | 22 +++++++---
 tests/conftest.py                             | 42 ++++++++++++++++---
 .../test_concat_with_subsetting_first.py      |  4 +-
 tests/unit/test_dataset_and_group_handling.py | 16 +++++--
 tests/unit/test_group_handling.py             |  9 ++--
 tests/unit/test_harmony_adapter.py            |  5 ++-
 tests/unit/test_run_stitchee.py               | 27 +++++++++---
 16 files changed, 212 insertions(+), 66 deletions(-)

diff --git a/concatenator/attribute_handling.py b/concatenator/attribute_handling.py
index 7d730e4..02ca021 100644
--- a/concatenator/attribute_handling.py
+++ b/concatenator/attribute_handling.py
@@ -1,5 +1,5 @@
 """Functions for converting "coordinates" in netCDF variable attributes
-    between paths that reference a group hierarchy and flattened paths.
+between paths that reference a group hierarchy and flattened paths.
 """
 
 import json
@@ -12,9 +12,13 @@
 import concatenator
 
 # Values needed for history_json attribute
-HISTORY_JSON_SCHEMA = "https://harmony.earthdata.nasa.gov/schemas/history/0.1.0/history-v0.1.0.json"
+HISTORY_JSON_SCHEMA = (
+    "https://harmony.earthdata.nasa.gov/schemas/history/0.1.0/history-v0.1.0.json"
+)
 PROGRAM = "stitchee"
-PROGRAM_REF = "https://cmr.earthdata.nasa.gov:443/search/concepts/S2940253910-LARC_CLOUD"
+PROGRAM_REF = (
+    "https://cmr.earthdata.nasa.gov:443/search/concepts/S2940253910-LARC_CLOUD"
+)
 VERSION = importlib_metadata.distribution("stitchee").version
 
 
diff --git a/concatenator/dataset_and_group_handling.py b/concatenator/dataset_and_group_handling.py
index d387137..bcd8178 100644
--- a/concatenator/dataset_and_group_handling.py
+++ b/concatenator/dataset_and_group_handling.py
@@ -52,9 +52,9 @@ def walk(
                 # Flatten the paths of variables referenced in the 'coordinates' attribute
                 flatten_coordinate_attribute_paths(new_dataset, var, var_group_name)
 
-                if (len(var.dimensions) == 1) and _string_dimension_name_pattern.fullmatch(
-                    var.dimensions[0]
-                ):
+                if (
+                    len(var.dimensions) == 1
+                ) and _string_dimension_name_pattern.fullmatch(var.dimensions[0]):
                     list_of_character_string_vars.append(var_group_name)
 
             # Delete variables
@@ -145,7 +145,9 @@ def flatten_grouped_dataset(
             if ensure_all_dims_are_coords and (
                 new_dim_name not in list(nc_dataset.variables.keys())
             ):
-                nc_dataset.createVariable(dim.name, datatype=np.int32, dimensions=(dim.name,))
+                nc_dataset.createVariable(
+                    dim.name, datatype=np.int32, dimensions=(dim.name,)
+                )
                 temporary_coordinate_variables.append(dim.name)
 
     list_of_character_string_vars: list[str] = []
@@ -185,7 +187,9 @@ def regroup_flattened_dataset(
         group_lst = []
         # need logic if there is data in the top level not in a group
         for var_name, _ in dataset.variables.items():
-            group_lst.append("/".join(str(var_name).split(concatenator.group_delim)[:-1]))
+            group_lst.append(
+                "/".join(str(var_name).split(concatenator.group_delim)[:-1])
+            )
         group_lst = ["/" if group == "" else group for group in group_lst]
         groups = set(group_lst)
         for group in groups:
@@ -226,9 +230,13 @@ def regroup_flattened_dataset(
                     new_var_dims = tuple(
                         str(d).rsplit(concatenator.group_delim, 1)[-1] for d in var.dims
                     )
-                    dim_sizes = [_get_dimension_size(base_dataset, dim) for dim in new_var_dims]
+                    dim_sizes = [
+                        _get_dimension_size(base_dataset, dim) for dim in new_var_dims
+                    ]
 
-                    chunk_sizes = _calculate_chunks(dim_sizes, default_low_dim_chunksize=4000)
+                    chunk_sizes = _calculate_chunks(
+                        dim_sizes, default_low_dim_chunksize=4000
+                    )
 
                 # Do the variable creation
                 if var.dtype == "O":
@@ -237,7 +245,11 @@ def regroup_flattened_dataset(
                     vartype = str(var.dtype)
 
                 compression: str | None = "zlib"
-                if vartype.startswith("<U") and len(var.shape) == 1 and var.shape[0] < 10:
+                if (
+                    vartype.startswith("<U")
+                    and len(var.shape) == 1
+                    and var.shape[0] < 10
+                ):
                     compression = None
 
                 var_group.createVariable(
@@ -269,7 +281,9 @@ def regroup_flattened_dataset(
 
 def _get_nested_group(dataset: nc.Dataset, group_path: str) -> nc.Group:
     nested_group = dataset
-    for group in group_path.strip(concatenator.group_delim).split(concatenator.group_delim)[:-1]:
+    for group in group_path.strip(concatenator.group_delim).split(
+        concatenator.group_delim
+    )[:-1]:
         nested_group = nested_group.groups[group]
     return nested_group
 
diff --git a/concatenator/dimension_cleanup.py b/concatenator/dimension_cleanup.py
index 3c70b17..3393bba 100644
--- a/concatenator/dimension_cleanup.py
+++ b/concatenator/dimension_cleanup.py
@@ -25,8 +25,12 @@ def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset:
 
     for var_name, var in nc_dataset.variables.items():
         dim_list = list(var.dimensions)
-        if len(set(dim_list)) != len(dim_list):  # get true if var.dimensions has a duplicate
-            dup_vars[var_name] = var  # populate dictionary with variables with vars with dup dims
+        if len(set(dim_list)) != len(
+            dim_list
+        ):  # get true if var.dimensions has a duplicate
+            dup_vars[var_name] = (
+                var  # populate dictionary with variables with vars with dup dims
+            )
 
     for dup_var_name, dup_var in dup_vars.items():
         dim_list = list(
@@ -35,7 +39,9 @@ def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset:
 
         # Dimension(s) that are duplicated are retrieved.
         #   Note: this is not yet tested for more than one duplicated dimension.
-        dim_dup = [item for item, count in collections.Counter(dim_list).items() if count > 1][0]
+        dim_dup = [
+            item for item, count in collections.Counter(dim_list).items() if count > 1
+        ][0]
         dim_dup_length = dup_var.shape[
             dup_var.dimensions.index(dim_dup)
         ]  # length of the duplicated dimension
@@ -53,7 +59,9 @@ def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset:
 
         # Attributes for the original variable are retrieved.
         attrs_contents = get_attributes_minus_fillvalue_and_renamed_coords(
-            original_var_name=dup_var_name, new_var_name=dim_dup_new, original_dataset=nc_dataset
+            original_var_name=dup_var_name,
+            new_var_name=dim_dup_new,
+            original_dataset=nc_dataset,
         )
         # for attrname in dup_var.ncattrs():
         #     if attrname != '_FillValue':
@@ -67,13 +75,11 @@ def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset:
 
         # Only create a new *Dimension* if it doesn't already exist.
         if dim_dup_new not in nc_dataset.dimensions.keys():
-
             # New dimension is created by copying from the duplicated dimension.
             nc_dataset.createDimension(dim_dup_new, dim_dup_length)
 
             # Only create a new dimension *Variable* if it existed originally in the NetCDF structure.
             if dim_dup in nc_dataset.variables.keys():
-
                 # New variable object is created for the renamed, previously duplicated dimension.
                 new_dup_var[dim_dup_new] = nc_dataset.createVariable(
                     dim_dup_new,
@@ -81,8 +87,12 @@ def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset:
                     (dim_dup_new,),
                     fill_value=fill_value,
                 )
-                dim_var_attr_contents = get_attributes_minus_fillvalue_and_renamed_coords(
-                    original_var_name=dim_dup, new_var_name=dim_dup_new, original_dataset=nc_dataset
+                dim_var_attr_contents = (
+                    get_attributes_minus_fillvalue_and_renamed_coords(
+                        original_var_name=dim_dup,
+                        new_var_name=dim_dup_new,
+                        original_dataset=nc_dataset,
+                    )
                 )
                 for attr_name, contents in dim_var_attr_contents.items():
                     new_dup_var[dim_dup_new].setncattr(attr_name, contents)
@@ -94,7 +104,10 @@ def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset:
 
         # Replace original *Variable* with new variable with no duplicated dimensions.
         new_dup_var[dup_var_name] = nc_dataset.createVariable(
-            dup_var_name, str(dup_var[:].dtype), tuple(new_dim_list), fill_value=fill_value
+            dup_var_name,
+            str(dup_var[:].dtype),
+            tuple(new_dim_list),
+            fill_value=fill_value,
         )
         for attr_name, contents in attrs_contents.items():
             new_dup_var[dup_var_name].setncattr(attr_name, contents)
@@ -111,7 +124,9 @@ def get_attributes_minus_fillvalue_and_renamed_coords(
 
     for ncattr in original_dataset.variables[original_var_name].ncattrs():
         if ncattr != "_FillValue":
-            contents: str = original_dataset.variables[original_var_name].getncattr(ncattr)
+            contents: str = original_dataset.variables[original_var_name].getncattr(
+                ncattr
+            )
             if ncattr == "coordinates":
                 contents.replace(original_var_name, new_var_name)
             attrs_contents[ncattr] = contents
diff --git a/concatenator/file_ops.py b/concatenator/file_ops.py
index 70e1094..0118500 100644
--- a/concatenator/file_ops.py
+++ b/concatenator/file_ops.py
@@ -22,7 +22,9 @@ def make_temp_dir_with_input_file_copies(
 ) -> tuple[list[str], str]:
     """Creates temporary directory and copies input files."""
     new_data_dir = Path(
-        add_label_to_path(str(output_path.parent / "temp_copy"), label=str(uuid.uuid4()))
+        add_label_to_path(
+            str(output_path.parent / "temp_copy"), label=str(uuid.uuid4())
+        )
     ).resolve()
     os.makedirs(new_data_dir, exist_ok=True)
     logger.info("Created temporary directory: %s", str(new_data_dir))
@@ -52,7 +54,9 @@ def validate_output_path(filepath: str, overwrite: bool = False) -> str:
                 f"Run again with `overwrite` option to overwrite existing file."
             )
     if path.is_dir():  # the specified path is an existing directory
-        raise TypeError("Output path cannot be a directory. Please specify a new filepath.")
+        raise TypeError(
+            "Output path cannot be a directory. Please specify a new filepath."
+        )
     return str(path)
 
 
diff --git a/concatenator/harmony/download_worker.py b/concatenator/harmony/download_worker.py
index fda43ab..7011029 100644
--- a/concatenator/harmony/download_worker.py
+++ b/concatenator/harmony/download_worker.py
@@ -13,7 +13,11 @@
 
 
 def multi_core_download(
-    urls: list, destination_dir: str, access_token: str, cfg: dict, process_count: int | None = None
+    urls: list,
+    destination_dir: str,
+    access_token: str,
+    cfg: dict,
+    process_count: int | None = None,
 ) -> list[Path]:
     """
     A method which automagically scales downloads to the number of CPU
@@ -74,7 +78,11 @@ def multi_core_download(
 
 
 def _download_worker(
-    url_queue: queue.Queue, path_list: list, destination_dir: str, access_token: str, cfg: dict
+    url_queue: queue.Queue,
+    path_list: list,
+    destination_dir: str,
+    access_token: str,
+    cfg: dict,
 ) -> None:
     """
     A method to be executed in a separate process which processes the url_queue
@@ -104,7 +112,9 @@ def _download_worker(
             break
 
         path = Path(
-            download(url, destination_dir, logger=logger, access_token=access_token, cfg=cfg)
+            download(
+                url, destination_dir, logger=logger, access_token=access_token, cfg=cfg
+            )
         )
         filename_match = re.match(r".*\/(.+\..+)", urlparse(url).path)
 
diff --git a/concatenator/harmony/service_adapter.py b/concatenator/harmony/service_adapter.py
index a91ef3f..720ce82 100644
--- a/concatenator/harmony/service_adapter.py
+++ b/concatenator/harmony/service_adapter.py
@@ -53,7 +53,9 @@ def invoke(self):
             # Message-only support is being depreciated in Harmony, so we should expect to
             # only see requests with catalogs when invoked with a newer Harmony instance
             # https://github.com/nasa/harmony-service-lib-py/blob/21bcfbda17caf626fb14d2ac4f8673be9726b549/harmony/adapter.py#L71
-            raise RuntimeError("Invoking Batchee without a STAC catalog is not supported")
+            raise RuntimeError(
+                "Invoking Batchee without a STAC catalog is not supported"
+            )
 
         return self.message, self.process_catalog(self.catalog)
 
@@ -104,7 +106,9 @@ def process_catalog(self, catalog: pystac.Catalog) -> pystac.Catalog:
                 history_json: list[dict] = []
                 for file_count, file in enumerate(input_files):
                     file_size = sizeof_fmt(file.stat().st_size)
-                    self.logger.info(f"File {file_count} is size <{file_size}>. Path={file}")
+                    self.logger.info(
+                        f"File {file_count} is size <{file_size}>. Path={file}"
+                    )
 
                     with nc.Dataset(file, "r") as dataset:
                         history_json.extend(retrieve_history(dataset))
@@ -134,14 +138,22 @@ def process_catalog(self, catalog: pystac.Catalog) -> pystac.Catalog:
             # -- Output to STAC catalog --
             result.clear_items()
             properties = dict(
-                start_datetime=datetimes["start_datetime"], end_datetime=datetimes["end_datetime"]
+                start_datetime=datetimes["start_datetime"],
+                end_datetime=datetimes["end_datetime"],
             )
 
             item = Item(
-                str(uuid4()), bbox_to_geometry(bounding_box), bounding_box, None, properties
+                str(uuid4()),
+                bbox_to_geometry(bounding_box),
+                bounding_box,
+                None,
+                properties,
             )
             asset = Asset(
-                staged_url, title=filename, media_type="application/x-netcdf4", roles=["data"]
+                staged_url,
+                title=filename,
+                media_type="application/x-netcdf4",
+                roles=["data"],
             )
             item.add_asset("data", asset)
             result.add_item(item)
diff --git a/concatenator/harmony/util.py b/concatenator/harmony/util.py
index a972aaf..2afa267 100644
--- a/concatenator/harmony/util.py
+++ b/concatenator/harmony/util.py
@@ -1,4 +1,5 @@
 """Misc utility functions"""
+
 from datetime import datetime
 
 from pystac import Asset, Item
@@ -78,7 +79,10 @@ def _get_output_date_range(input_items: list[Item]) -> dict[str, str]:
         start_datetime = min(start_datetime, new_start_datetime)
         end_datetime = max(end_datetime, new_end_datetime)
 
-    return {"start_datetime": start_datetime.isoformat(), "end_datetime": end_datetime.isoformat()}
+    return {
+        "start_datetime": start_datetime.isoformat(),
+        "end_datetime": end_datetime.isoformat(),
+    }
 
 
 def _get_item_date_range(item: Item) -> tuple[datetime, datetime]:
diff --git a/concatenator/run_stitchee.py b/concatenator/run_stitchee.py
index cfa5f2f..16bed85 100644
--- a/concatenator/run_stitchee.py
+++ b/concatenator/run_stitchee.py
@@ -93,7 +93,10 @@ def parse_args(args: list) -> argparse.Namespace:
         default="__",
     )
     parser.add_argument(
-        "-O", "--overwrite", action="store_true", help="Overwrite output file if it already exists."
+        "-O",
+        "--overwrite",
+        action="store_true",
+        help="Overwrite output file if it already exists.",
     )
     parser.add_argument(
         "-v",
diff --git a/concatenator/stitchee.py b/concatenator/stitchee.py
index 50da058..be4d25a 100644
--- a/concatenator/stitchee.py
+++ b/concatenator/stitchee.py
@@ -88,7 +88,11 @@ def stitchee(
     concatenator.group_delim = group_delimiter
 
     intermediate_flat_filepaths: list[str] = []
-    benchmark_log = {"flattening": 0.0, "concatenating": 0.0, "reconstructing_groups": 0.0}
+    benchmark_log = {
+        "flattening": 0.0,
+        "concatenating": 0.0,
+        "reconstructing_groups": 0.0,
+    }
 
     # Proceed to concatenate only files that are workable (can be opened and are not empty).
     input_files, num_input_files = validate_workable_files(files_to_concat, logger)
@@ -103,7 +107,9 @@ def stitchee(
     # Exit cleanly with the file copied if one workable netCDF file found.
     if num_input_files == 1:
         shutil.copyfile(input_files[0], output_file)
-        logger.info("One workable netCDF file. Copied to output path without modification.")
+        logger.info(
+            "One workable netCDF file. Copied to output path without modification."
+        )
         return output_file
 
     if concat_dim and (concat_method == "xarray-combine"):
@@ -123,14 +129,15 @@ def stitchee(
         # Instead of "with nc.Dataset() as" inside the loop, we use a context manager stack.
         # This way all files are cleanly closed outside the loop.
         with ExitStack() as context_stack:
-
             logger.info("Flattening all input files...")
             xrdataset_list = []
             concat_dim_order = []
             for i, filepath in enumerate(input_files):
                 # The group structure is flattened.
                 start_time = time.time()
-                logger.info("    ..file %03d/%03d <%s>..", i + 1, num_input_files, filepath)
+                logger.info(
+                    "    ..file %03d/%03d <%s>..", i + 1, num_input_files, filepath
+                )
 
                 ncfile = context_stack.enter_context(nc.Dataset(filepath, "r+"))
 
@@ -171,7 +178,9 @@ def stitchee(
             # Reorder the xarray datasets according to the concat dim values.
             xrdataset_list = [
                 dataset
-                for _, dataset in sorted(zip(concat_dim_order, xrdataset_list), key=lambda x: x[0])
+                for _, dataset in sorted(
+                    zip(concat_dim_order, xrdataset_list), key=lambda x: x[0]
+                )
             ]
 
             # Flattened files are concatenated together (Using XARRAY).
diff --git a/docs/tutorial_examples.ipynb b/docs/tutorial_examples.ipynb
index ef8f601..e1bdc8b 100644
--- a/docs/tutorial_examples.ipynb
+++ b/docs/tutorial_examples.ipynb
@@ -417,7 +417,11 @@
     "    ds_geo = xr.open_dataset(filepath, group=\"geolocation\")\n",
     "\n",
     "    if index < 0:\n",
-    "        X, Y, C = ds_geo.longitude.values, ds_geo.latitude.values, ds_product[product_name].values\n",
+    "        X, Y, C = (\n",
+    "            ds_geo.longitude.values,\n",
+    "            ds_geo.latitude.values,\n",
+    "            ds_product[product_name].values,\n",
+    "        )\n",
     "        filename = filepath\n",
     "    else:\n",
     "        X, Y, C = (\n",
@@ -445,11 +449,19 @@
     "\n",
     "    ax.set_extent(extent, crs=proj)\n",
     "\n",
-    "    ax.add_feature(cfeature.COASTLINE.with_scale(\"10m\"), linewidth=0.1, edgecolor=\"dimgray\")\n",
-    "    ax.add_feature(cfeature.OCEAN, linewidth=0.1, edgecolor=\"dimgray\", facecolor=\"lightsteelblue\")\n",
-    "    ax.add_feature(cfeature.LAKES, linewidth=0.1, edgecolor=\"dimgray\", facecolor=\"lightsteelblue\")\n",
+    "    ax.add_feature(\n",
+    "        cfeature.COASTLINE.with_scale(\"10m\"), linewidth=0.1, edgecolor=\"dimgray\"\n",
+    "    )\n",
+    "    ax.add_feature(\n",
+    "        cfeature.OCEAN, linewidth=0.1, edgecolor=\"dimgray\", facecolor=\"lightsteelblue\"\n",
+    "    )\n",
+    "    ax.add_feature(\n",
+    "        cfeature.LAKES, linewidth=0.1, edgecolor=\"dimgray\", facecolor=\"lightsteelblue\"\n",
+    "    )\n",
     "    ax.add_feature(cfeature.BORDERS, linewidth=0.1, edgecolor=\"dimgray\")\n",
-    "    ax.add_feature(cfeature.STATES.with_scale(\"10m\"), linewidth=0.1, edgecolor=\"dimgray\")\n",
+    "    ax.add_feature(\n",
+    "        cfeature.STATES.with_scale(\"10m\"), linewidth=0.1, edgecolor=\"dimgray\"\n",
+    "    )\n",
     "\n",
     "    (H, xbins, ybins) = h2d\n",
     "    H = H.T\n",
diff --git a/tests/conftest.py b/tests/conftest.py
index 457b43a..2d35f90 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -96,7 +96,9 @@ def toy_empty_dataset(temp_toy_data_dir):
     return filepath
 
 
-def add_to_ds_3dims_3vars_4coords_1group_with_step_values(open_ds: nc.Dataset, step_values: list):
+def add_to_ds_3dims_3vars_4coords_1group_with_step_values(
+    open_ds: nc.Dataset, step_values: list
+):
     """Creates groups, dimensions, variables; and uses chosen step values in an open dataset"""
     grp1 = open_ds.createGroup("Group1")
 
@@ -126,9 +128,33 @@ def add_to_ds_3dims_3vars_4coords_1group_with_step_values(open_ds: nc.Dataset, s
         [200, 300, 400, 500, 600, 700, 800],
     ]
     grp1["var2"][:] = [
-        [[200, 150], [300, 150], [400, 150], [500, 150], [600, 150], [700, 150], [800, 150]],
-        [[200, 150], [300, 150], [400, 150], [500, 150], [600, 150], [700, 150], [800, 150]],
-        [[200, 150], [300, 150], [400, 150], [500, 150], [600, 150], [700, 150], [800, 150]],
+        [
+            [200, 150],
+            [300, 150],
+            [400, 150],
+            [500, 150],
+            [600, 150],
+            [700, 150],
+            [800, 150],
+        ],
+        [
+            [200, 150],
+            [300, 150],
+            [400, 150],
+            [500, 150],
+            [600, 150],
+            [700, 150],
+            [800, 150],
+        ],
+        [
+            [200, 150],
+            [300, 150],
+            [400, 150],
+            [500, 150],
+            [600, 150],
+            [700, 150],
+            [800, 150],
+        ],
     ]
 
     return open_ds
@@ -139,7 +165,9 @@ def ds_3dims_3vars_4coords_1group_part1(temp_toy_data_dir) -> Path:
     filepath = temp_toy_data_dir / "test_3dims_3vars_4coords_1group_part1.nc"
 
     f = nc.Dataset(filename=filepath, mode="w")
-    f = add_to_ds_3dims_3vars_4coords_1group_with_step_values(f, step_values=[9, 10, 11])
+    f = add_to_ds_3dims_3vars_4coords_1group_with_step_values(
+        f, step_values=[9, 10, 11]
+    )
     f.close()
 
     return filepath
@@ -150,7 +178,9 @@ def ds_3dims_3vars_4coords_1group_part2(temp_toy_data_dir):
     filepath = temp_toy_data_dir / "test_3dims_3vars_4coords_1group_part2.nc"
 
     f = nc.Dataset(filename=filepath, mode="w")
-    f = add_to_ds_3dims_3vars_4coords_1group_with_step_values(f, step_values=[12, 13, 14])
+    f = add_to_ds_3dims_3vars_4coords_1group_with_step_values(
+        f, step_values=[12, 13, 14]
+    )
     f.close()
 
     return filepath
diff --git a/tests/integration/test_concat_with_subsetting_first.py b/tests/integration/test_concat_with_subsetting_first.py
index a045224..14b1182 100644
--- a/tests/integration/test_concat_with_subsetting_first.py
+++ b/tests/integration/test_concat_with_subsetting_first.py
@@ -36,7 +36,9 @@ def test_concat_with_subsetting_first(temp_output_dir):
     output_path = stitchee(
         file_names,
         output_file=str(
-            (temp_output_dir / "output_harmony_subsetting_to_stitchee_test.nc").resolve()
+            (
+                temp_output_dir / "output_harmony_subsetting_to_stitchee_test.nc"
+            ).resolve()
         ),
         concat_dim="mirror_step",
         concat_method="xarray-concat",
diff --git a/tests/unit/test_dataset_and_group_handling.py b/tests/unit/test_dataset_and_group_handling.py
index a99526c..c7fc6d4 100644
--- a/tests/unit/test_dataset_and_group_handling.py
+++ b/tests/unit/test_dataset_and_group_handling.py
@@ -15,9 +15,13 @@
 def test_dataset_with_single_empty_input_file():
     """Ensure that a dataset with a single empty input file is propagating empty granule to the output"""
     files_to_concat = [
-        data_for_tests_dir / "unit-test-data" / "TEMPO_NO2_L2_V03_20240328T154353Z_S008G01.nc4"
+        data_for_tests_dir
+        / "unit-test-data"
+        / "TEMPO_NO2_L2_V03_20240328T154353Z_S008G01.nc4"
     ]
-    workable_files, number_of_workable_files = validate_workable_files(files_to_concat, None)
+    workable_files, number_of_workable_files = validate_workable_files(
+        files_to_concat, None
+    )
     assert number_of_workable_files == 1
 
 
@@ -32,13 +36,17 @@ def test_dataset_with_singleton_null_values_is_identified_as_empty():
         assert _is_file_empty(ds)
 
 
-def test_toy_dataset_with_singleton_null_values_is_identified_as_empty(toy_empty_dataset):
+def test_toy_dataset_with_singleton_null_values_is_identified_as_empty(
+    toy_empty_dataset,
+):
     """Ensure that a dataset with only null arrays with 1-length dimensions is identified as empty."""
     with nc.Dataset(toy_empty_dataset) as ds:
         assert _is_file_empty(ds)
 
 
-def test_dataset_with_values_is_identified_as_not_empty(ds_3dims_3vars_4coords_1group_part1):
+def test_dataset_with_values_is_identified_as_not_empty(
+    ds_3dims_3vars_4coords_1group_part1,
+):
     """Ensure that a dataset with non-null arrays is identified as NOT empty."""
     with nc.Dataset(ds_3dims_3vars_4coords_1group_part1) as ds:
         assert _is_file_empty(ds) is False
diff --git a/tests/unit/test_group_handling.py b/tests/unit/test_group_handling.py
index 53cb094..7adde93 100644
--- a/tests/unit/test_group_handling.py
+++ b/tests/unit/test_group_handling.py
@@ -23,13 +23,16 @@ class TestGroupHandling:
     def test_workable_files_validation(self, temp_output_dir):
         filepaths = [
             path_str(
-                self.__granules_path, "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4"
+                self.__granules_path,
+                "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4",
             ),
             path_str(
-                self.__granules_path, "TEMPO_NO2_L2_V03_20240601T211614Z_S012G02_subsetted.nc4"
+                self.__granules_path,
+                "TEMPO_NO2_L2_V03_20240601T211614Z_S012G02_subsetted.nc4",
             ),
             path_str(
-                self.__granules_path, "TEMPO_NO2_L2_V03_20240601T212254Z_S012G03_subsetted.nc4"
+                self.__granules_path,
+                "TEMPO_NO2_L2_V03_20240601T212254Z_S012G03_subsetted.nc4",
             ),
         ]
 
diff --git a/tests/unit/test_harmony_adapter.py b/tests/unit/test_harmony_adapter.py
index 73eb183..30135f7 100644
--- a/tests/unit/test_harmony_adapter.py
+++ b/tests/unit/test_harmony_adapter.py
@@ -26,7 +26,6 @@ def test_service_invoke(self, temp_output_dir):
 
         # test with both paged catalogs and un-paged catalogs
         for in_catalog_name in ["catalog.json", "catalog0.json"]:
-
             # Copy granule files, because Dataset's variable names are modified during flattening.
             # If stitchee is run two times on the same file, it will likely fail the second time.
             _ = prep_input_files(self.__granules_path, self.__granule_copies_path)
@@ -64,7 +63,9 @@ def test_service_invoke(self, temp_output_dir):
             out_catalog_path = temp_output_dir.joinpath("catalog.json")
             out_catalog = json.loads(out_catalog_path.read_text())
 
-            item_meta = next(item for item in out_catalog["links"] if item["rel"] == "item")
+            item_meta = next(
+                item for item in out_catalog["links"] if item["rel"] == "item"
+            )
             item_href = item_meta["href"]
             item_path = temp_output_dir.joinpath(item_href).resolve()
 
diff --git a/tests/unit/test_run_stitchee.py b/tests/unit/test_run_stitchee.py
index 96c2006..1c67c52 100644
--- a/tests/unit/test_run_stitchee.py
+++ b/tests/unit/test_run_stitchee.py
@@ -11,7 +11,15 @@
 
 def test_parser():
     parsed = parse_args(
-        ["ncfile1", "ncfile2", "ncfile3", "-o", "outfile", "--concat_dim", "mirror_step"]
+        [
+            "ncfile1",
+            "ncfile2",
+            "ncfile3",
+            "-o",
+            "outfile",
+            "--concat_dim",
+            "mirror_step",
+        ]
     )
 
     assert parsed.input == ["ncfile1", "ncfile2", "ncfile3"]
@@ -23,13 +31,18 @@ def test_parser():
 
 @pytest.mark.usefixtures("pass_options")
 class TestBatching:
-
     def test_run_stitchee_cli_with_three_filepaths(self, temp_output_dir):
         test_args = [
             concatenator.run_stitchee.__file__,
-            path_str(granules_path, "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4"),
-            path_str(granules_path, "TEMPO_NO2_L2_V03_20240601T211614Z_S012G02_subsetted.nc4"),
-            path_str(granules_path, "TEMPO_NO2_L2_V03_20240601T212254Z_S012G03_subsetted.nc4"),
+            path_str(
+                granules_path, "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4"
+            ),
+            path_str(
+                granules_path, "TEMPO_NO2_L2_V03_20240601T211614Z_S012G02_subsetted.nc4"
+            ),
+            path_str(
+                granules_path, "TEMPO_NO2_L2_V03_20240601T212254Z_S012G03_subsetted.nc4"
+            ),
             "--copy_input_files",
             "--verbose",
             "-o",
@@ -63,7 +76,9 @@ def test_run_stitchee_cli_with_one_directorypath(self, temp_output_dir):
     def test_run_stitchee_cli_with_one_netCDFpath(self, temp_output_dir):
         test_args = [
             concatenator.run_stitchee.__file__,
-            path_str(granules_path, "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4"),
+            path_str(
+                granules_path, "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4"
+            ),
             "--copy_input_files",
             "--verbose",
             "-o",

From 7a2908f658e2ae21447c375709763b4c21777508 Mon Sep 17 00:00:00 2001
From: Daniel Kaufman <114174502+danielfromearth@users.noreply.github.com>
Date: Fri, 15 Nov 2024 12:00:26 -0500
Subject: [PATCH 03/37] Update CHANGELOG.md

---
 CHANGELOG.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 86f105c..e7a4365 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Common Changelog](https://common-changelog.org/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## Unreleased
+
+### Changed
+- update pre commit: to autoupdate and with gitleaks ([#247](https://github.com/nasa/stitchee/pull/247))([**@danielfromearth**](https://github.com/danielfromearth))
+
 ## [1.5.0] - 2024-10-28
 
 ### Changed

From 739cfb3a0d91b4fa5f885adebb523c04fa7b22cf Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Fri, 15 Nov 2024 12:04:09 -0500
Subject: [PATCH 04/37] remove dependency on black in group=dev and poetry
 update

---
 poetry.lock    | 988 +++++++++++++++++++++++--------------------------
 pyproject.toml |   1 -
 2 files changed, 468 insertions(+), 521 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index aa7c636..9283504 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand.
 
 [[package]]
 name = "appnope"
@@ -83,83 +83,36 @@ charset-normalizer = ["charset-normalizer"]
 html5lib = ["html5lib"]
 lxml = ["lxml"]
 
-[[package]]
-name = "black"
-version = "24.10.0"
-description = "The uncompromising code formatter."
-optional = false
-python-versions = ">=3.9"
-files = [
-    {file = "black-24.10.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e6668650ea4b685440857138e5fe40cde4d652633b1bdffc62933d0db4ed9812"},
-    {file = "black-24.10.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:1c536fcf674217e87b8cc3657b81809d3c085d7bf3ef262ead700da345bfa6ea"},
-    {file = "black-24.10.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:649fff99a20bd06c6f727d2a27f401331dc0cc861fb69cde910fe95b01b5928f"},
-    {file = "black-24.10.0-cp310-cp310-win_amd64.whl", hash = "sha256:fe4d6476887de70546212c99ac9bd803d90b42fc4767f058a0baa895013fbb3e"},
-    {file = "black-24.10.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:5a2221696a8224e335c28816a9d331a6c2ae15a2ee34ec857dcf3e45dbfa99ad"},
-    {file = "black-24.10.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:f9da3333530dbcecc1be13e69c250ed8dfa67f43c4005fb537bb426e19200d50"},
-    {file = "black-24.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:4007b1393d902b48b36958a216c20c4482f601569d19ed1df294a496eb366392"},
-    {file = "black-24.10.0-cp311-cp311-win_amd64.whl", hash = "sha256:394d4ddc64782e51153eadcaaca95144ac4c35e27ef9b0a42e121ae7e57a9175"},
-    {file = "black-24.10.0-cp312-cp312-macosx_10_13_x86_64.whl", hash = "sha256:b5e39e0fae001df40f95bd8cc36b9165c5e2ea88900167bddf258bacef9bbdc3"},
-    {file = "black-24.10.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:d37d422772111794b26757c5b55a3eade028aa3fde43121ab7b673d050949d65"},
-    {file = "black-24.10.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:14b3502784f09ce2443830e3133dacf2c0110d45191ed470ecb04d0f5f6fcb0f"},
-    {file = "black-24.10.0-cp312-cp312-win_amd64.whl", hash = "sha256:30d2c30dc5139211dda799758559d1b049f7f14c580c409d6ad925b74a4208a8"},
-    {file = "black-24.10.0-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:1cbacacb19e922a1d75ef2b6ccaefcd6e93a2c05ede32f06a21386a04cedb981"},
-    {file = "black-24.10.0-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:1f93102e0c5bb3907451063e08b9876dbeac810e7da5a8bfb7aeb5a9ef89066b"},
-    {file = "black-24.10.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:ddacb691cdcdf77b96f549cf9591701d8db36b2f19519373d60d31746068dbf2"},
-    {file = "black-24.10.0-cp313-cp313-win_amd64.whl", hash = "sha256:680359d932801c76d2e9c9068d05c6b107f2584b2a5b88831c83962eb9984c1b"},
-    {file = "black-24.10.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:17374989640fbca88b6a448129cd1745c5eb8d9547b464f281b251dd00155ccd"},
-    {file = "black-24.10.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:63f626344343083322233f175aaf372d326de8436f5928c042639a4afbbf1d3f"},
-    {file = "black-24.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:ccfa1d0cb6200857f1923b602f978386a3a2758a65b52e0950299ea014be6800"},
-    {file = "black-24.10.0-cp39-cp39-win_amd64.whl", hash = "sha256:2cd9c95431d94adc56600710f8813ee27eea544dd118d45896bb734e9d7a0dc7"},
-    {file = "black-24.10.0-py3-none-any.whl", hash = "sha256:3bb2b7a1f7b685f85b11fed1ef10f8a9148bceb49853e47a294a3dd963c1dd7d"},
-    {file = "black-24.10.0.tar.gz", hash = "sha256:846ea64c97afe3bc677b761787993be4991810ecc7a4a937816dd6bddedc4875"},
-]
-
-[package.dependencies]
-click = ">=8.0.0"
-mypy-extensions = ">=0.4.3"
-packaging = ">=22.0"
-pathspec = ">=0.9.0"
-platformdirs = ">=2"
-tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
-typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""}
-
-[package.extras]
-colorama = ["colorama (>=0.4.3)"]
-d = ["aiohttp (>=3.10)"]
-jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
-uvloop = ["uvloop (>=0.15.2)"]
-
 [[package]]
 name = "bleach"
-version = "6.1.0"
+version = "6.2.0"
 description = "An easy safelist-based HTML-sanitizing tool."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "bleach-6.1.0-py3-none-any.whl", hash = "sha256:3225f354cfc436b9789c66c4ee030194bee0568fbf9cbdad3bc8b5c26c5f12b6"},
-    {file = "bleach-6.1.0.tar.gz", hash = "sha256:0a31f1837963c41d46bbf1331b8778e1308ea0791db03cc4e7357b97cf42a8fe"},
+    {file = "bleach-6.2.0-py3-none-any.whl", hash = "sha256:117d9c6097a7c3d22fd578fcd8d35ff1e125df6736f554da4e432fdd63f31e5e"},
+    {file = "bleach-6.2.0.tar.gz", hash = "sha256:123e894118b8a599fd80d3ec1a6d4cc7ce4e5882b1317a7e1ba69b56e95f991f"},
 ]
 
 [package.dependencies]
-six = ">=1.9.0"
 webencodings = "*"
 
 [package.extras]
-css = ["tinycss2 (>=1.1.0,<1.3)"]
+css = ["tinycss2 (>=1.1.0,<1.5)"]
 
 [[package]]
 name = "boto3"
-version = "1.35.44"
+version = "1.35.62"
 description = "The AWS SDK for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "boto3-1.35.44-py3-none-any.whl", hash = "sha256:18416d07b41e6094101a44f8b881047dcec6b846dad0b9f83b9bbf2f0cd93d07"},
-    {file = "boto3-1.35.44.tar.gz", hash = "sha256:7f8e8a252458d584d8cf7877c372c4f74ec103356eedf43d2dd9e479f47f3639"},
+    {file = "boto3-1.35.62-py3-none-any.whl", hash = "sha256:e6574047701ab009c2b2bb17b530a3a2fb34de8698b77f8bbb34dd0c9286c117"},
+    {file = "boto3-1.35.62.tar.gz", hash = "sha256:f80eefe7506aa01799b1027d03eddfd3c4a60548d6db5c32f139e1dec9f3f4f5"},
 ]
 
 [package.dependencies]
-botocore = ">=1.35.44,<1.36.0"
+botocore = ">=1.35.62,<1.36.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.10.0,<0.11.0"
 
@@ -168,13 +121,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "botocore"
-version = "1.35.44"
+version = "1.35.62"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -277,41 +230,47 @@ pycparser = "*"
 
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 description = "Time-handling functionality from netcdf4-python"
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 [package.dependencies]
@@ -478,73 +437,73 @@ test = ["pytest"]
 
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 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.9"
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 [package.dependencies]
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 ]
 
 [[package]]
@@ -723,13 +682,13 @@ examples = ["boto3 (>=1.28,<2.0)", "intake-stac (>=0.4.0,<0.5.0)", "ipyplot (>=1
 
 [[package]]
 name = "harmony-service-lib"
-version = "2.2.0"
+version = "2.3.0"
 description = "A library for Python-based Harmony services to parse incoming message, fetch data, stage data, and call back to Harmony."
 optional = false
 python-versions = ">=3.9"
 files = [
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 [package.dependencies]
@@ -742,7 +701,7 @@ requests = ">=2.24,<3.0"
 urllib3 = ">=1.26.9,<1.27.0"
 
 [package.extras]
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 [[package]]
 name = "idna"
@@ -827,13 +786,13 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio
 
 [[package]]
 name = "ipython"
-version = "8.28.0"
+version = "8.29.0"
 description = "IPython: Productive Interactive Computing"
 optional = false
 python-versions = ">=3.10"
 files = [
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 ]
 
 [package.dependencies]
@@ -865,22 +824,22 @@ test-extra = ["curio", "ipython[test]", "matplotlib (!=3.2.0)", "nbformat", "num
 
 [[package]]
 name = "jedi"
-version = "0.19.1"
+version = "0.19.2"
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 ]
 
 [package.dependencies]
-parso = ">=0.8.3,<0.9.0"
+parso = ">=0.8.4,<0.9.0"
 
 [package.extras]
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 qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
-testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
+testing = ["Django", "attrs", "colorama", "docopt", "pytest (<9.0.0)"]
 
 [[package]]
 name = "jinja2"
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 [[package]]
@@ -2502,141 +2463,128 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "rpds-py"
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 optional = false
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+    {file = "tinycss2-1.4.0.tar.gz", hash = "sha256:10c0972f6fc0fbee87c3edb76549357415e94548c1ae10ebccdea16fb404a9b7"},
 ]
 
 [package.dependencies]
@@ -2790,13 +2738,13 @@ test = ["pytest", "ruff"]
 
 [[package]]
 name = "tomli"
-version = "2.0.2"
+version = "2.1.0"
 description = "A lil' TOML parser"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "tomli-2.0.2-py3-none-any.whl", hash = "sha256:2ebe24485c53d303f690b0ec092806a085f07af5a5aa1464f3931eec36caaa38"},
-    {file = "tomli-2.0.2.tar.gz", hash = "sha256:d46d457a85337051c36524bc5349dd91b1877838e2979ac5ced3e710ed8a60ed"},
+    {file = "tomli-2.1.0-py3-none-any.whl", hash = "sha256:a5c57c3d1c56f5ccdf89f6523458f60ef716e210fc47c4cfb188c5ba473e0391"},
+    {file = "tomli-2.1.0.tar.gz", hash = "sha256:3f646cae2aec94e17d04973e4249548320197cfabdf130015d023de4b74d8ab8"},
 ]
 
 [[package]]
@@ -2874,41 +2822,41 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
 name = "watchdog"
-version = "5.0.3"
+version = "6.0.0"
 description = "Filesystem events monitoring"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "watchdog-5.0.3-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:85527b882f3facda0579bce9d743ff7f10c3e1e0db0a0d0e28170a7d0e5ce2ea"},
-    {file = "watchdog-5.0.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:53adf73dcdc0ef04f7735066b4a57a4cd3e49ef135daae41d77395f0b5b692cb"},
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-    {file = "watchdog-5.0.3-py3-none-manylinux2014_s390x.whl", hash = "sha256:26dd201857d702bdf9d78c273cafcab5871dd29343748524695cecffa44a8d97"},
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-    {file = "watchdog-5.0.3-py3-none-win_amd64.whl", hash = "sha256:f00b4cf737f568be9665563347a910f8bdc76f88c2970121c86243c8cfdf90e9"},
-    {file = "watchdog-5.0.3-py3-none-win_ia64.whl", hash = "sha256:49f4d36cb315c25ea0d946e018c01bb028048023b9e103d3d3943f58e109dd45"},
-    {file = "watchdog-5.0.3.tar.gz", hash = "sha256:108f42a7f0345042a854d4d0ad0834b741d421330d5f575b81cb27b883500176"},
+    {file = "watchdog-6.0.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:d1cdb490583ebd691c012b3d6dae011000fe42edb7a82ece80965b42abd61f26"},
+    {file = "watchdog-6.0.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:bc64ab3bdb6a04d69d4023b29422170b74681784ffb9463ed4870cf2f3e66112"},
+    {file = "watchdog-6.0.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c897ac1b55c5a1461e16dae288d22bb2e412ba9807df8397a635d88f671d36c3"},
+    {file = "watchdog-6.0.0-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:6eb11feb5a0d452ee41f824e271ca311a09e250441c262ca2fd7ebcf2461a06c"},
+    {file = "watchdog-6.0.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:ef810fbf7b781a5a593894e4f439773830bdecb885e6880d957d5b9382a960d2"},
+    {file = "watchdog-6.0.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:afd0fe1b2270917c5e23c2a65ce50c2a4abb63daafb0d419fde368e272a76b7c"},
+    {file = "watchdog-6.0.0-cp312-cp312-macosx_10_13_universal2.whl", hash = "sha256:bdd4e6f14b8b18c334febb9c4425a878a2ac20efd1e0b231978e7b150f92a948"},
+    {file = "watchdog-6.0.0-cp312-cp312-macosx_10_13_x86_64.whl", hash = "sha256:c7c15dda13c4eb00d6fb6fc508b3c0ed88b9d5d374056b239c4ad1611125c860"},
+    {file = "watchdog-6.0.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:6f10cb2d5902447c7d0da897e2c6768bca89174d0c6e1e30abec5421af97a5b0"},
+    {file = "watchdog-6.0.0-cp313-cp313-macosx_10_13_universal2.whl", hash = "sha256:490ab2ef84f11129844c23fb14ecf30ef3d8a6abafd3754a6f75ca1e6654136c"},
+    {file = "watchdog-6.0.0-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:76aae96b00ae814b181bb25b1b98076d5fc84e8a53cd8885a318b42b6d3a5134"},
+    {file = "watchdog-6.0.0-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:a175f755fc2279e0b7312c0035d52e27211a5bc39719dd529625b1930917345b"},
+    {file = "watchdog-6.0.0-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:e6f0e77c9417e7cd62af82529b10563db3423625c5fce018430b249bf977f9e8"},
+    {file = "watchdog-6.0.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:90c8e78f3b94014f7aaae121e6b909674df5b46ec24d6bebc45c44c56729af2a"},
+    {file = "watchdog-6.0.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:e7631a77ffb1f7d2eefa4445ebbee491c720a5661ddf6df3498ebecae5ed375c"},
+    {file = "watchdog-6.0.0-pp310-pypy310_pp73-macosx_10_15_x86_64.whl", hash = "sha256:c7ac31a19f4545dd92fc25d200694098f42c9a8e391bc00bdd362c5736dbf881"},
+    {file = "watchdog-6.0.0-pp310-pypy310_pp73-macosx_11_0_arm64.whl", hash = "sha256:9513f27a1a582d9808cf21a07dae516f0fab1cf2d7683a742c498b93eedabb11"},
+    {file = "watchdog-6.0.0-pp39-pypy39_pp73-macosx_10_15_x86_64.whl", hash = "sha256:7a0e56874cfbc4b9b05c60c8a1926fedf56324bb08cfbc188969777940aef3aa"},
+    {file = "watchdog-6.0.0-pp39-pypy39_pp73-macosx_11_0_arm64.whl", hash = "sha256:e6439e374fc012255b4ec786ae3c4bc838cd7309a540e5fe0952d03687d8804e"},
+    {file = "watchdog-6.0.0-py3-none-manylinux2014_aarch64.whl", hash = "sha256:7607498efa04a3542ae3e05e64da8202e58159aa1fa4acddf7678d34a35d4f13"},
+    {file = "watchdog-6.0.0-py3-none-manylinux2014_armv7l.whl", hash = "sha256:9041567ee8953024c83343288ccc458fd0a2d811d6a0fd68c4c22609e3490379"},
+    {file = "watchdog-6.0.0-py3-none-manylinux2014_i686.whl", hash = "sha256:82dc3e3143c7e38ec49d61af98d6558288c415eac98486a5c581726e0737c00e"},
+    {file = "watchdog-6.0.0-py3-none-manylinux2014_ppc64.whl", hash = "sha256:212ac9b8bf1161dc91bd09c048048a95ca3a4c4f5e5d4a7d1b1a7d5752a7f96f"},
+    {file = "watchdog-6.0.0-py3-none-manylinux2014_ppc64le.whl", hash = "sha256:e3df4cbb9a450c6d49318f6d14f4bbc80d763fa587ba46ec86f99f9e6876bb26"},
+    {file = "watchdog-6.0.0-py3-none-manylinux2014_s390x.whl", hash = "sha256:2cce7cfc2008eb51feb6aab51251fd79b85d9894e98ba847408f662b3395ca3c"},
+    {file = "watchdog-6.0.0-py3-none-manylinux2014_x86_64.whl", hash = "sha256:20ffe5b202af80ab4266dcd3e91aae72bf2da48c0d33bdb15c66658e685e94e2"},
+    {file = "watchdog-6.0.0-py3-none-win32.whl", hash = "sha256:07df1fdd701c5d4c8e55ef6cf55b8f0120fe1aef7ef39a1c6fc6bc2e606d517a"},
+    {file = "watchdog-6.0.0-py3-none-win_amd64.whl", hash = "sha256:cbafb470cf848d93b5d013e2ecb245d4aa1c8fd0504e863ccefa32445359d680"},
+    {file = "watchdog-6.0.0-py3-none-win_ia64.whl", hash = "sha256:a1914259fa9e1454315171103c6a30961236f508b9b623eae470268bbcc6a22f"},
+    {file = "watchdog-6.0.0.tar.gz", hash = "sha256:9ddf7c82fda3ae8e24decda1338ede66e1c99883db93711d8fb941eaa2d8c282"},
 ]
 
 [package.extras]
@@ -2963,13 +2911,13 @@ viz = ["cartopy", "matplotlib", "nc-time-axis", "seaborn"]
 
 [[package]]
 name = "zipp"
-version = "3.20.2"
+version = "3.21.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"},
-    {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"},
+    {file = "zipp-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931"},
+    {file = "zipp-3.21.0.tar.gz", hash = "sha256:2c9958f6430a2040341a52eb608ed6dd93ef4392e02ffe219417c1b28b5dd1f4"},
 ]
 
 [package.extras]
@@ -2983,4 +2931,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "89162224f9ea8aff9560180bdd4d7ba97cfcd03709c6226f2960bad7c298896f"
+content-hash = "1c00406c6349b930437b8ee2e0d3cb82606acb29076b36da34548b6ea13cf6fb"
diff --git a/pyproject.toml b/pyproject.toml
index 4189703..d716c07 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -27,7 +27,6 @@ importlib-metadata = ">=8.4.0"
 [tool.poetry.group.dev.dependencies]
 pytest = ">=8.1.1"
 mypy = ">=1.9.0"
-black = ">=24.4.0"
 ruff = ">=0.5.0"
 pytest-cov = ">=5.0.0"
 mkdocs = ">=1.6.0"

From 38db147fdf32bcf67b74a69b1ebabb5ec26cad62 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Fri, 15 Nov 2024 12:05:04 -0500
Subject: [PATCH 05/37] temporary, work in progress commit

---
 concatenator/dataset_and_group_handling.py    |  5 ++
 .../test_concat_with_subsetting_first.py      | 64 +++++++++++++++++++
 tests/unit/test_dataset_and_group_handling.py | 22 +++++++
 3 files changed, 91 insertions(+)

diff --git a/concatenator/dataset_and_group_handling.py b/concatenator/dataset_and_group_handling.py
index d387137..892ccec 100644
--- a/concatenator/dataset_and_group_handling.py
+++ b/concatenator/dataset_and_group_handling.py
@@ -268,6 +268,11 @@ def regroup_flattened_dataset(
 
 
 def _get_nested_group(dataset: nc.Dataset, group_path: str) -> nc.Group:
+    """Get the group object that is represented by the group_path string.
+
+    If the 'group_path' string represents a dimension in the root group,
+    then this returns the root group.
+    """
     nested_group = dataset
     for group in group_path.strip(concatenator.group_delim).split(concatenator.group_delim)[:-1]:
         nested_group = nested_group.groups[group]
diff --git a/tests/integration/test_concat_with_subsetting_first.py b/tests/integration/test_concat_with_subsetting_first.py
index a045224..c46b2a3 100644
--- a/tests/integration/test_concat_with_subsetting_first.py
+++ b/tests/integration/test_concat_with_subsetting_first.py
@@ -37,6 +37,70 @@ def test_concat_with_subsetting_first(temp_output_dir):
         file_names,
         output_file=str(
             (temp_output_dir / "output_harmony_subsetting_to_stitchee_test.nc").resolve()
+            #         ),
+            #         concat_dim="mirror_step",
+            #         concat_method="xarray-concat",
+            #         write_tmp_flat_concatenated=True,
+            #         keep_tmp_files=True,
+            #     )
+            #
+            #     assert output_path
+            #
+            # C1262899916-LARC_CLOUD
+            #
+            # G1269044803-LARC_CLOUD
+            # G1269044708-LARC_CLOUD
+            # G1269044681-LARC_CLOUD
+            # G1269044688-LARC_CLOUD
+            # G1269044514-LARC_CLOUD
+            # G1269044741-LARC_CLOUD
+            # G1269044710-LARC_CLOUD
+            # G1269044439-LARC_CLOUD
+            # G1269044715-LARC_CLOUD
+            # G1269044815-LARC_CLOUD
+            # G1269044726-LARC_CLOUD
+            # G1269044787-LARC_CLOUD
+            # G1269044827-LARC_CLOUD
+            # G1269044658-LARC_CLOUD
+            # G1269044679-LARC_CLOUD
+            # G1269044727-LARC_CLOUD
+            # subset=lat(32.56485%3A42.82943)&
+            # subset=lon(-135.7248%3A-52.76692)&
+            # subset=time(%222024-08-02T00%3A00%3A00.000Z%22%3A%222024-08-02T10%3A39%3A37.000Z%22)&
+            # concatenate=true&skipPreview=true
+            #
+            # def test_concat_with_subsetting_first(temp_output_dir):
+            #     """Subsets 4 granules from the TEMPO NO2 collection, and then concatenates them."""
+            #     harmony_client = Client()
+            #
+            #     # "Nitrogen Dioxide total column"
+            #     request = Request(
+            #         collection=Collection(id="C2930725014-LARC_CLOUD"),
+            #         temporal={
+            #             "start": dt.datetime(2024, 5, 13, 11, 0, 0),
+            #             "stop": dt.datetime(2024, 5, 13, 20, 0, 0),
+            #         },
+            #         spatial=BBox(-130, 30, -115, 35),
+            #         concatenate=False,
+            #     )
+            #     if not request.is_valid():
+            #         raise RuntimeError
+            #
+            #     # Submit and wait for job to complete.
+            #     job_id = harmony_client.submit(request)
+            #     print(f"Job ID: {job_id}")
+            #     harmony_client.wait_for_processing(job_id, show_progress=False)
+            #
+            #     # Download the result files.
+            #     futures = harmony_client.download_all(job_id, directory=str(temp_output_dir))
+            #     file_names = [f.result() for f in futures]
+            #     print(f"File names: {file_names}")
+            #
+            #     # Try concatenating the resulting files
+            #     output_path = stitchee(
+            #         file_names,
+            #         output_file=str(
+            #             (temp_output_dir / "output_harmony_subsetting_to_stitchee_test.nc").resolve()
         ),
         concat_dim="mirror_step",
         concat_method="xarray-concat",
diff --git a/tests/unit/test_dataset_and_group_handling.py b/tests/unit/test_dataset_and_group_handling.py
index a99526c..a9bf746 100644
--- a/tests/unit/test_dataset_and_group_handling.py
+++ b/tests/unit/test_dataset_and_group_handling.py
@@ -5,6 +5,7 @@
 import netCDF4 as nc
 
 from concatenator.dataset_and_group_handling import (
+    _get_nested_group,
     _is_file_empty,
     validate_workable_files,
 )
@@ -42,3 +43,24 @@ def test_dataset_with_values_is_identified_as_not_empty(ds_3dims_3vars_4coords_1
     """Ensure that a dataset with non-null arrays is identified as NOT empty."""
     with nc.Dataset(ds_3dims_3vars_4coords_1group_part1) as ds:
         assert _is_file_empty(ds) is False
+
+
+def test_get_nested_group(ds_3dims_3vars_4coords_1group_part1):
+    """Ensure that the retrieved group is correct."""
+    with nc.Dataset(ds_3dims_3vars_4coords_1group_part1) as ds:
+        group_obj = _get_nested_group(ds, "__Group1__level")
+        assert isinstance(group_obj, nc.Group)
+
+
+def test_get_root_group(ds_3dims_3vars_4coords_1group_part1):
+    """Ensure that the retrieved group is correct."""
+    with nc.Dataset(ds_3dims_3vars_4coords_1group_part1) as ds:
+        group_obj = _get_nested_group(ds, "__track")
+        assert group_obj == ds
+
+
+def test_get_root_group_when_no_delimiter_present(ds_3dims_3vars_4coords_1group_part1):
+    """Ensure that the retrieved group is correct."""
+    with nc.Dataset(ds_3dims_3vars_4coords_1group_part1) as ds:
+        group_obj = _get_nested_group(ds, "track")
+        assert group_obj == ds

From 08b17fef21b53840da0f8bce5b5cca237bfe4710 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Fri, 15 Nov 2024 12:08:03 -0500
Subject: [PATCH 06/37] remove now unused section for black from pyproject.toml

---
 pyproject.toml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index d716c07..553a22a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,9 +50,6 @@ build-backend = "poetry.core.masonry.api"
 module = "netCDF4.*"
 ignore_missing_imports = true
 
-[tool.black]
-line-length = 100
-
 [tool.ruff]
 builtins = ["ellipsis"]
 exclude = [
@@ -60,6 +57,8 @@ exclude = [
   "doc",
   "_typed_ops.pyi",
 ]
+# Allow lines to be as long as 100.
+line-length = 100
 target-version = "py310"
 
 [tool.ruff.lint]

From 4a6c5593a21f4a8a617b19b5b88f7a4a82fefad0 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Fri, 15 Nov 2024 12:10:08 -0500
Subject: [PATCH 07/37] remove badge for black from README.md

---
 README.md | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/README.md b/README.md
index 4744689..55fbc4c 100644
--- a/README.md
+++ b/README.md
@@ -11,9 +11,6 @@
     <a href='https://stitchee.readthedocs.io/en/latest/?badge=latest'>
         <img src='https://readthedocs.org/projects/stitchee/badge/?version=latest' alt='Documentation Status' />
     </a>
-    <a href="https://github.com/python/black" target="_blank">
-        <img src="https://img.shields.io/badge/code%20style-black-000000.svg" alt="Code style">
-    </a>
     <a href="http://mypy-lang.org/" target="_blank">
         <img src="http://www.mypy-lang.org/static/mypy_badge.svg" alt="Mypy checked">
     </a>

From a0ff697946872e4f1023f18b6a6affe1b6e22c54 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 15 Nov 2024 17:11:15 +0000
Subject: [PATCH 08/37] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 concatenator/attribute_handling.py            |  8 ++---
 concatenator/dataset_and_group_handling.py    | 32 ++++++-------------
 concatenator/dimension_cleanup.py             | 26 +++++----------
 concatenator/file_ops.py                      |  8 ++---
 concatenator/harmony/download_worker.py       |  4 +--
 concatenator/harmony/service_adapter.py       |  8 ++---
 concatenator/stitchee.py                      | 12 ++-----
 docs/tutorial_examples.ipynb                  | 16 +++-------
 tests/conftest.py                             | 12 ++-----
 .../test_concat_with_subsetting_first.py      |  4 +--
 tests/unit/test_dataset_and_group_handling.py |  8 ++---
 tests/unit/test_harmony_adapter.py            |  4 +--
 tests/unit/test_run_stitchee.py               | 16 +++-------
 13 files changed, 42 insertions(+), 116 deletions(-)

diff --git a/concatenator/attribute_handling.py b/concatenator/attribute_handling.py
index 02ca021..d4a3833 100644
--- a/concatenator/attribute_handling.py
+++ b/concatenator/attribute_handling.py
@@ -12,13 +12,9 @@
 import concatenator
 
 # Values needed for history_json attribute
-HISTORY_JSON_SCHEMA = (
-    "https://harmony.earthdata.nasa.gov/schemas/history/0.1.0/history-v0.1.0.json"
-)
+HISTORY_JSON_SCHEMA = "https://harmony.earthdata.nasa.gov/schemas/history/0.1.0/history-v0.1.0.json"
 PROGRAM = "stitchee"
-PROGRAM_REF = (
-    "https://cmr.earthdata.nasa.gov:443/search/concepts/S2940253910-LARC_CLOUD"
-)
+PROGRAM_REF = "https://cmr.earthdata.nasa.gov:443/search/concepts/S2940253910-LARC_CLOUD"
 VERSION = importlib_metadata.distribution("stitchee").version
 
 
diff --git a/concatenator/dataset_and_group_handling.py b/concatenator/dataset_and_group_handling.py
index bcd8178..d387137 100644
--- a/concatenator/dataset_and_group_handling.py
+++ b/concatenator/dataset_and_group_handling.py
@@ -52,9 +52,9 @@ def walk(
                 # Flatten the paths of variables referenced in the 'coordinates' attribute
                 flatten_coordinate_attribute_paths(new_dataset, var, var_group_name)
 
-                if (
-                    len(var.dimensions) == 1
-                ) and _string_dimension_name_pattern.fullmatch(var.dimensions[0]):
+                if (len(var.dimensions) == 1) and _string_dimension_name_pattern.fullmatch(
+                    var.dimensions[0]
+                ):
                     list_of_character_string_vars.append(var_group_name)
 
             # Delete variables
@@ -145,9 +145,7 @@ def flatten_grouped_dataset(
             if ensure_all_dims_are_coords and (
                 new_dim_name not in list(nc_dataset.variables.keys())
             ):
-                nc_dataset.createVariable(
-                    dim.name, datatype=np.int32, dimensions=(dim.name,)
-                )
+                nc_dataset.createVariable(dim.name, datatype=np.int32, dimensions=(dim.name,))
                 temporary_coordinate_variables.append(dim.name)
 
     list_of_character_string_vars: list[str] = []
@@ -187,9 +185,7 @@ def regroup_flattened_dataset(
         group_lst = []
         # need logic if there is data in the top level not in a group
         for var_name, _ in dataset.variables.items():
-            group_lst.append(
-                "/".join(str(var_name).split(concatenator.group_delim)[:-1])
-            )
+            group_lst.append("/".join(str(var_name).split(concatenator.group_delim)[:-1]))
         group_lst = ["/" if group == "" else group for group in group_lst]
         groups = set(group_lst)
         for group in groups:
@@ -230,13 +226,9 @@ def regroup_flattened_dataset(
                     new_var_dims = tuple(
                         str(d).rsplit(concatenator.group_delim, 1)[-1] for d in var.dims
                     )
-                    dim_sizes = [
-                        _get_dimension_size(base_dataset, dim) for dim in new_var_dims
-                    ]
+                    dim_sizes = [_get_dimension_size(base_dataset, dim) for dim in new_var_dims]
 
-                    chunk_sizes = _calculate_chunks(
-                        dim_sizes, default_low_dim_chunksize=4000
-                    )
+                    chunk_sizes = _calculate_chunks(dim_sizes, default_low_dim_chunksize=4000)
 
                 # Do the variable creation
                 if var.dtype == "O":
@@ -245,11 +237,7 @@ def regroup_flattened_dataset(
                     vartype = str(var.dtype)
 
                 compression: str | None = "zlib"
-                if (
-                    vartype.startswith("<U")
-                    and len(var.shape) == 1
-                    and var.shape[0] < 10
-                ):
+                if vartype.startswith("<U") and len(var.shape) == 1 and var.shape[0] < 10:
                     compression = None
 
                 var_group.createVariable(
@@ -281,9 +269,7 @@ def regroup_flattened_dataset(
 
 def _get_nested_group(dataset: nc.Dataset, group_path: str) -> nc.Group:
     nested_group = dataset
-    for group in group_path.strip(concatenator.group_delim).split(
-        concatenator.group_delim
-    )[:-1]:
+    for group in group_path.strip(concatenator.group_delim).split(concatenator.group_delim)[:-1]:
         nested_group = nested_group.groups[group]
     return nested_group
 
diff --git a/concatenator/dimension_cleanup.py b/concatenator/dimension_cleanup.py
index 3393bba..1d5ef10 100644
--- a/concatenator/dimension_cleanup.py
+++ b/concatenator/dimension_cleanup.py
@@ -25,12 +25,8 @@ def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset:
 
     for var_name, var in nc_dataset.variables.items():
         dim_list = list(var.dimensions)
-        if len(set(dim_list)) != len(
-            dim_list
-        ):  # get true if var.dimensions has a duplicate
-            dup_vars[var_name] = (
-                var  # populate dictionary with variables with vars with dup dims
-            )
+        if len(set(dim_list)) != len(dim_list):  # get true if var.dimensions has a duplicate
+            dup_vars[var_name] = var  # populate dictionary with variables with vars with dup dims
 
     for dup_var_name, dup_var in dup_vars.items():
         dim_list = list(
@@ -39,9 +35,7 @@ def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset:
 
         # Dimension(s) that are duplicated are retrieved.
         #   Note: this is not yet tested for more than one duplicated dimension.
-        dim_dup = [
-            item for item, count in collections.Counter(dim_list).items() if count > 1
-        ][0]
+        dim_dup = [item for item, count in collections.Counter(dim_list).items() if count > 1][0]
         dim_dup_length = dup_var.shape[
             dup_var.dimensions.index(dim_dup)
         ]  # length of the duplicated dimension
@@ -87,12 +81,10 @@ def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset:
                     (dim_dup_new,),
                     fill_value=fill_value,
                 )
-                dim_var_attr_contents = (
-                    get_attributes_minus_fillvalue_and_renamed_coords(
-                        original_var_name=dim_dup,
-                        new_var_name=dim_dup_new,
-                        original_dataset=nc_dataset,
-                    )
+                dim_var_attr_contents = get_attributes_minus_fillvalue_and_renamed_coords(
+                    original_var_name=dim_dup,
+                    new_var_name=dim_dup_new,
+                    original_dataset=nc_dataset,
                 )
                 for attr_name, contents in dim_var_attr_contents.items():
                     new_dup_var[dim_dup_new].setncattr(attr_name, contents)
@@ -124,9 +116,7 @@ def get_attributes_minus_fillvalue_and_renamed_coords(
 
     for ncattr in original_dataset.variables[original_var_name].ncattrs():
         if ncattr != "_FillValue":
-            contents: str = original_dataset.variables[original_var_name].getncattr(
-                ncattr
-            )
+            contents: str = original_dataset.variables[original_var_name].getncattr(ncattr)
             if ncattr == "coordinates":
                 contents.replace(original_var_name, new_var_name)
             attrs_contents[ncattr] = contents
diff --git a/concatenator/file_ops.py b/concatenator/file_ops.py
index 0118500..70e1094 100644
--- a/concatenator/file_ops.py
+++ b/concatenator/file_ops.py
@@ -22,9 +22,7 @@ def make_temp_dir_with_input_file_copies(
 ) -> tuple[list[str], str]:
     """Creates temporary directory and copies input files."""
     new_data_dir = Path(
-        add_label_to_path(
-            str(output_path.parent / "temp_copy"), label=str(uuid.uuid4())
-        )
+        add_label_to_path(str(output_path.parent / "temp_copy"), label=str(uuid.uuid4()))
     ).resolve()
     os.makedirs(new_data_dir, exist_ok=True)
     logger.info("Created temporary directory: %s", str(new_data_dir))
@@ -54,9 +52,7 @@ def validate_output_path(filepath: str, overwrite: bool = False) -> str:
                 f"Run again with `overwrite` option to overwrite existing file."
             )
     if path.is_dir():  # the specified path is an existing directory
-        raise TypeError(
-            "Output path cannot be a directory. Please specify a new filepath."
-        )
+        raise TypeError("Output path cannot be a directory. Please specify a new filepath.")
     return str(path)
 
 
diff --git a/concatenator/harmony/download_worker.py b/concatenator/harmony/download_worker.py
index 7011029..68c177d 100644
--- a/concatenator/harmony/download_worker.py
+++ b/concatenator/harmony/download_worker.py
@@ -112,9 +112,7 @@ def _download_worker(
             break
 
         path = Path(
-            download(
-                url, destination_dir, logger=logger, access_token=access_token, cfg=cfg
-            )
+            download(url, destination_dir, logger=logger, access_token=access_token, cfg=cfg)
         )
         filename_match = re.match(r".*\/(.+\..+)", urlparse(url).path)
 
diff --git a/concatenator/harmony/service_adapter.py b/concatenator/harmony/service_adapter.py
index 720ce82..9c3c7b5 100644
--- a/concatenator/harmony/service_adapter.py
+++ b/concatenator/harmony/service_adapter.py
@@ -53,9 +53,7 @@ def invoke(self):
             # Message-only support is being depreciated in Harmony, so we should expect to
             # only see requests with catalogs when invoked with a newer Harmony instance
             # https://github.com/nasa/harmony-service-lib-py/blob/21bcfbda17caf626fb14d2ac4f8673be9726b549/harmony/adapter.py#L71
-            raise RuntimeError(
-                "Invoking Batchee without a STAC catalog is not supported"
-            )
+            raise RuntimeError("Invoking Batchee without a STAC catalog is not supported")
 
         return self.message, self.process_catalog(self.catalog)
 
@@ -106,9 +104,7 @@ def process_catalog(self, catalog: pystac.Catalog) -> pystac.Catalog:
                 history_json: list[dict] = []
                 for file_count, file in enumerate(input_files):
                     file_size = sizeof_fmt(file.stat().st_size)
-                    self.logger.info(
-                        f"File {file_count} is size <{file_size}>. Path={file}"
-                    )
+                    self.logger.info(f"File {file_count} is size <{file_size}>. Path={file}")
 
                     with nc.Dataset(file, "r") as dataset:
                         history_json.extend(retrieve_history(dataset))
diff --git a/concatenator/stitchee.py b/concatenator/stitchee.py
index be4d25a..9da96f4 100644
--- a/concatenator/stitchee.py
+++ b/concatenator/stitchee.py
@@ -107,9 +107,7 @@ def stitchee(
     # Exit cleanly with the file copied if one workable netCDF file found.
     if num_input_files == 1:
         shutil.copyfile(input_files[0], output_file)
-        logger.info(
-            "One workable netCDF file. Copied to output path without modification."
-        )
+        logger.info("One workable netCDF file. Copied to output path without modification.")
         return output_file
 
     if concat_dim and (concat_method == "xarray-combine"):
@@ -135,9 +133,7 @@ def stitchee(
             for i, filepath in enumerate(input_files):
                 # The group structure is flattened.
                 start_time = time.time()
-                logger.info(
-                    "    ..file %03d/%03d <%s>..", i + 1, num_input_files, filepath
-                )
+                logger.info("    ..file %03d/%03d <%s>..", i + 1, num_input_files, filepath)
 
                 ncfile = context_stack.enter_context(nc.Dataset(filepath, "r+"))
 
@@ -178,9 +174,7 @@ def stitchee(
             # Reorder the xarray datasets according to the concat dim values.
             xrdataset_list = [
                 dataset
-                for _, dataset in sorted(
-                    zip(concat_dim_order, xrdataset_list), key=lambda x: x[0]
-                )
+                for _, dataset in sorted(zip(concat_dim_order, xrdataset_list), key=lambda x: x[0])
             ]
 
             # Flattened files are concatenated together (Using XARRAY).
diff --git a/docs/tutorial_examples.ipynb b/docs/tutorial_examples.ipynb
index e1bdc8b..7bd17ab 100644
--- a/docs/tutorial_examples.ipynb
+++ b/docs/tutorial_examples.ipynb
@@ -449,19 +449,11 @@
     "\n",
     "    ax.set_extent(extent, crs=proj)\n",
     "\n",
-    "    ax.add_feature(\n",
-    "        cfeature.COASTLINE.with_scale(\"10m\"), linewidth=0.1, edgecolor=\"dimgray\"\n",
-    "    )\n",
-    "    ax.add_feature(\n",
-    "        cfeature.OCEAN, linewidth=0.1, edgecolor=\"dimgray\", facecolor=\"lightsteelblue\"\n",
-    "    )\n",
-    "    ax.add_feature(\n",
-    "        cfeature.LAKES, linewidth=0.1, edgecolor=\"dimgray\", facecolor=\"lightsteelblue\"\n",
-    "    )\n",
+    "    ax.add_feature(cfeature.COASTLINE.with_scale(\"10m\"), linewidth=0.1, edgecolor=\"dimgray\")\n",
+    "    ax.add_feature(cfeature.OCEAN, linewidth=0.1, edgecolor=\"dimgray\", facecolor=\"lightsteelblue\")\n",
+    "    ax.add_feature(cfeature.LAKES, linewidth=0.1, edgecolor=\"dimgray\", facecolor=\"lightsteelblue\")\n",
     "    ax.add_feature(cfeature.BORDERS, linewidth=0.1, edgecolor=\"dimgray\")\n",
-    "    ax.add_feature(\n",
-    "        cfeature.STATES.with_scale(\"10m\"), linewidth=0.1, edgecolor=\"dimgray\"\n",
-    "    )\n",
+    "    ax.add_feature(cfeature.STATES.with_scale(\"10m\"), linewidth=0.1, edgecolor=\"dimgray\")\n",
     "\n",
     "    (H, xbins, ybins) = h2d\n",
     "    H = H.T\n",
diff --git a/tests/conftest.py b/tests/conftest.py
index 2d35f90..b3399c2 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -96,9 +96,7 @@ def toy_empty_dataset(temp_toy_data_dir):
     return filepath
 
 
-def add_to_ds_3dims_3vars_4coords_1group_with_step_values(
-    open_ds: nc.Dataset, step_values: list
-):
+def add_to_ds_3dims_3vars_4coords_1group_with_step_values(open_ds: nc.Dataset, step_values: list):
     """Creates groups, dimensions, variables; and uses chosen step values in an open dataset"""
     grp1 = open_ds.createGroup("Group1")
 
@@ -165,9 +163,7 @@ def ds_3dims_3vars_4coords_1group_part1(temp_toy_data_dir) -> Path:
     filepath = temp_toy_data_dir / "test_3dims_3vars_4coords_1group_part1.nc"
 
     f = nc.Dataset(filename=filepath, mode="w")
-    f = add_to_ds_3dims_3vars_4coords_1group_with_step_values(
-        f, step_values=[9, 10, 11]
-    )
+    f = add_to_ds_3dims_3vars_4coords_1group_with_step_values(f, step_values=[9, 10, 11])
     f.close()
 
     return filepath
@@ -178,9 +174,7 @@ def ds_3dims_3vars_4coords_1group_part2(temp_toy_data_dir):
     filepath = temp_toy_data_dir / "test_3dims_3vars_4coords_1group_part2.nc"
 
     f = nc.Dataset(filename=filepath, mode="w")
-    f = add_to_ds_3dims_3vars_4coords_1group_with_step_values(
-        f, step_values=[12, 13, 14]
-    )
+    f = add_to_ds_3dims_3vars_4coords_1group_with_step_values(f, step_values=[12, 13, 14])
     f.close()
 
     return filepath
diff --git a/tests/integration/test_concat_with_subsetting_first.py b/tests/integration/test_concat_with_subsetting_first.py
index 14b1182..a045224 100644
--- a/tests/integration/test_concat_with_subsetting_first.py
+++ b/tests/integration/test_concat_with_subsetting_first.py
@@ -36,9 +36,7 @@ def test_concat_with_subsetting_first(temp_output_dir):
     output_path = stitchee(
         file_names,
         output_file=str(
-            (
-                temp_output_dir / "output_harmony_subsetting_to_stitchee_test.nc"
-            ).resolve()
+            (temp_output_dir / "output_harmony_subsetting_to_stitchee_test.nc").resolve()
         ),
         concat_dim="mirror_step",
         concat_method="xarray-concat",
diff --git a/tests/unit/test_dataset_and_group_handling.py b/tests/unit/test_dataset_and_group_handling.py
index c7fc6d4..34abb0b 100644
--- a/tests/unit/test_dataset_and_group_handling.py
+++ b/tests/unit/test_dataset_and_group_handling.py
@@ -15,13 +15,9 @@
 def test_dataset_with_single_empty_input_file():
     """Ensure that a dataset with a single empty input file is propagating empty granule to the output"""
     files_to_concat = [
-        data_for_tests_dir
-        / "unit-test-data"
-        / "TEMPO_NO2_L2_V03_20240328T154353Z_S008G01.nc4"
+        data_for_tests_dir / "unit-test-data" / "TEMPO_NO2_L2_V03_20240328T154353Z_S008G01.nc4"
     ]
-    workable_files, number_of_workable_files = validate_workable_files(
-        files_to_concat, None
-    )
+    workable_files, number_of_workable_files = validate_workable_files(files_to_concat, None)
     assert number_of_workable_files == 1
 
 
diff --git a/tests/unit/test_harmony_adapter.py b/tests/unit/test_harmony_adapter.py
index 30135f7..ac5ec34 100644
--- a/tests/unit/test_harmony_adapter.py
+++ b/tests/unit/test_harmony_adapter.py
@@ -63,9 +63,7 @@ def test_service_invoke(self, temp_output_dir):
             out_catalog_path = temp_output_dir.joinpath("catalog.json")
             out_catalog = json.loads(out_catalog_path.read_text())
 
-            item_meta = next(
-                item for item in out_catalog["links"] if item["rel"] == "item"
-            )
+            item_meta = next(item for item in out_catalog["links"] if item["rel"] == "item")
             item_href = item_meta["href"]
             item_path = temp_output_dir.joinpath(item_href).resolve()
 
diff --git a/tests/unit/test_run_stitchee.py b/tests/unit/test_run_stitchee.py
index 1c67c52..37badfd 100644
--- a/tests/unit/test_run_stitchee.py
+++ b/tests/unit/test_run_stitchee.py
@@ -34,15 +34,9 @@ class TestBatching:
     def test_run_stitchee_cli_with_three_filepaths(self, temp_output_dir):
         test_args = [
             concatenator.run_stitchee.__file__,
-            path_str(
-                granules_path, "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4"
-            ),
-            path_str(
-                granules_path, "TEMPO_NO2_L2_V03_20240601T211614Z_S012G02_subsetted.nc4"
-            ),
-            path_str(
-                granules_path, "TEMPO_NO2_L2_V03_20240601T212254Z_S012G03_subsetted.nc4"
-            ),
+            path_str(granules_path, "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4"),
+            path_str(granules_path, "TEMPO_NO2_L2_V03_20240601T211614Z_S012G02_subsetted.nc4"),
+            path_str(granules_path, "TEMPO_NO2_L2_V03_20240601T212254Z_S012G03_subsetted.nc4"),
             "--copy_input_files",
             "--verbose",
             "-o",
@@ -76,9 +70,7 @@ def test_run_stitchee_cli_with_one_directorypath(self, temp_output_dir):
     def test_run_stitchee_cli_with_one_netCDFpath(self, temp_output_dir):
         test_args = [
             concatenator.run_stitchee.__file__,
-            path_str(
-                granules_path, "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4"
-            ),
+            path_str(granules_path, "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4"),
             "--copy_input_files",
             "--verbose",
             "-o",

From 88d41d839f49229ecbc657a46394b124b42075c6 Mon Sep 17 00:00:00 2001
From: stitchee bot <stitchee@noreply.github.com>
Date: Fri, 15 Nov 2024 17:20:44 +0000
Subject: [PATCH 09/37] /version 1.6.0a4

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 553a22a..748194f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "stitchee"
-version = "1.6.0a3"
+version = "1.6.0a4"
 description = "NetCDF4 Along-existing-dimension Concatenation Service"
 authors = ["Daniel Kaufman <daniel.kaufman@nasa.gov>"]
 readme = "README.md"

From d4aea53d03ec8727be20e33e11ebd1a2139eb37b Mon Sep 17 00:00:00 2001
From: stitchee bot <stitchee@noreply.github.com>
Date: Fri, 15 Nov 2024 19:22:01 +0000
Subject: [PATCH 10/37] /version 1.6.0a5

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 748194f..5bfdd36 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "stitchee"
-version = "1.6.0a4"
+version = "1.6.0a5"
 description = "NetCDF4 Along-existing-dimension Concatenation Service"
 authors = ["Daniel Kaufman <daniel.kaufman@nasa.gov>"]
 readme = "README.md"

From 3018a6b5af813e2f33246cb6ef4bba3121b2b84e Mon Sep 17 00:00:00 2001
From: stitchee bot <stitchee@noreply.github.com>
Date: Fri, 15 Nov 2024 19:35:44 +0000
Subject: [PATCH 11/37] /version 1.7.0a0

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 5bfdd36..b95b68e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "stitchee"
-version = "1.6.0a5"
+version = "1.7.0a0"
 description = "NetCDF4 Along-existing-dimension Concatenation Service"
 authors = ["Daniel Kaufman <daniel.kaufman@nasa.gov>"]
 readme = "README.md"

From 5562901b09f2d2f2aab5bcede2fdfd4997c923b7 Mon Sep 17 00:00:00 2001
From: stitchee bot <stitchee@noreply.github.com>
Date: Fri, 15 Nov 2024 19:37:24 +0000
Subject: [PATCH 12/37] /version 1.6.0rc1

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 5bfdd36..02e4ef1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "stitchee"
-version = "1.6.0a5"
+version = "1.6.0rc1"
 description = "NetCDF4 Along-existing-dimension Concatenation Service"
 authors = ["Daniel Kaufman <daniel.kaufman@nasa.gov>"]
 readme = "README.md"

From 4dfa4612fda2b601005f5e1f01aa16b0d5ec671f Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Tue, 19 Nov 2024 11:43:24 -0500
Subject: [PATCH 13/37] add unit test for
 get_attributes_minus_fillvalue_and_renamed_coords() and fix test names

---
 concatenator/dimension_cleanup.py             | 12 +--
 tests/conftest.py                             | 92 +++++++++++++++++--
 tests/unit/test_dataset_and_group_handling.py | 16 ++--
 tests/unit/test_dimension_cleanup.py          | 29 ++++++
 4 files changed, 125 insertions(+), 24 deletions(-)
 create mode 100644 tests/unit/test_dimension_cleanup.py

diff --git a/concatenator/dimension_cleanup.py b/concatenator/dimension_cleanup.py
index 1d5ef10..0220eca 100644
--- a/concatenator/dimension_cleanup.py
+++ b/concatenator/dimension_cleanup.py
@@ -31,7 +31,7 @@ def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset:
     for dup_var_name, dup_var in dup_vars.items():
         dim_list = list(
             dup_var.dimensions
-        )  # original dimensions of the variable with duplicated dims
+        )  # original dimensions of the variable with duplicated dimensions
 
         # Dimension(s) that are duplicated are retrieved.
         #   Note: this is not yet tested for more than one duplicated dimension.
@@ -95,15 +95,15 @@ def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset:
         del nc_dataset.variables[dup_var_name]
 
         # Replace original *Variable* with new variable with no duplicated dimensions.
-        new_dup_var[dup_var_name] = nc_dataset.createVariable(
+        nc_dataset.variables[dup_var_name] = nc_dataset.createVariable(
             dup_var_name,
             str(dup_var[:].dtype),
             tuple(new_dim_list),
             fill_value=fill_value,
         )
         for attr_name, contents in attrs_contents.items():
-            new_dup_var[dup_var_name].setncattr(attr_name, contents)
-        new_dup_var[dup_var_name][:] = dup_var[:]
+            nc_dataset[dup_var_name].setncattr(attr_name, contents)
+        nc_dataset[dup_var_name][:] = dup_var[:]
 
     return nc_dataset
 
@@ -111,14 +111,14 @@ def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset:
 def get_attributes_minus_fillvalue_and_renamed_coords(
     original_var_name: str, new_var_name: str, original_dataset: nc.Dataset
 ) -> dict:
-    """Variable attributes are retrieved."""
+    """Variable attributes (other than FillValue) are retrieved."""
     attrs_contents = {}
 
     for ncattr in original_dataset.variables[original_var_name].ncattrs():
         if ncattr != "_FillValue":
             contents: str = original_dataset.variables[original_var_name].getncattr(ncattr)
             if ncattr == "coordinates":
-                contents.replace(original_var_name, new_var_name)
+                contents = contents.replace(original_var_name, new_var_name)
             attrs_contents[ncattr] = contents
 
     return attrs_contents
diff --git a/tests/conftest.py b/tests/conftest.py
index b3399c2..be1c071 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -96,7 +96,57 @@ def toy_empty_dataset(temp_toy_data_dir):
     return filepath
 
 
-def add_to_ds_3dims_3vars_4coords_1group_with_step_values(open_ds: nc.Dataset, step_values: list):
+def add_to_ds_3dims_3vars_2coords_nogroup(open_ds: nc.Dataset, step_values: list):
+    """Creates groups, dimensions, variables; and uses chosen step values in an open dataset"""
+    # Root-level Dimensions/Variables
+    open_ds.createDimension("step", 3)
+    open_ds.createDimension("track", 7)
+    open_ds.createVariable("step", "i2", ("step",), fill_value=False)
+    open_ds.createVariable("track", "i2", ("track",), fill_value=False)
+    open_ds.createVariable("var0", "f4", ("step", "track"))
+    #
+    open_ds["step"][:] = step_values
+    open_ds["track"][:] = [1, 2, 3, 4, 5, 6, 7]
+    open_ds["var0"][:] = [
+        [33, 78, 65, 12, 85, 35, 44],
+        [64, 24, 87, 12, 54, 82, 24],
+        [66, 18, 99, 52, 77, 88, 59],
+    ]
+
+    open_ds["var0"].coordinates = "var0 track"
+
+    return open_ds
+
+
+def add_to_ds_3dims_3vars_2coords_nogroup_duplicate_dimensions(
+    open_ds: nc.Dataset, step_values: list
+):
+    """Creates groups, dimensions, variables; and uses chosen step values in an open dataset"""
+    # Root-level Dimensions/Variables
+    open_ds.createDimension("step", 3)
+    open_ds.createDimension("track", 7)
+    open_ds.createVariable("step", "i2", ("step",), fill_value=False)
+    open_ds.createVariable("track", "i2", ("track",), fill_value=False)
+    open_ds.createVariable("var0", "f4", ("track", "step", "step"), fill_value=-99)
+    #
+    open_ds["step"][:] = step_values
+    open_ds["track"][:] = [1, 2, 3, 4, 5, 6, 7]
+    open_ds["var0"][:] = [
+        [[33, 78, 65], [33, 78, 65], [33, 78, 65]],
+        [[64, 24, 87], [64, 24, 87], [64, 24, 87]],
+        [[66, 18, 99], [66, 18, 99], [66, 18, 99]],
+        [[77, 88, 59], [77, 88, 59], [77, 88, 59]],
+        [[52, 77, 88], [52, 77, 88], [52, 77, 88]],
+        [[66, 18, 99], [66, 18, 99], [66, 18, 99]],
+        [[18, 99, 52], [18, 99, 52], [18, 99, 52]],
+    ]
+
+    open_ds["var0"].coordinates = "track step step"
+
+    return open_ds
+
+
+def add_to_ds_3dims_3vars_3coords_1group_with_step_values(open_ds: nc.Dataset, step_values: list):
     """Creates groups, dimensions, variables; and uses chosen step values in an open dataset"""
     grp1 = open_ds.createGroup("Group1")
 
@@ -159,33 +209,55 @@ def add_to_ds_3dims_3vars_4coords_1group_with_step_values(open_ds: nc.Dataset, s
 
 
 @pytest.fixture(scope="function")
-def ds_3dims_3vars_4coords_1group_part1(temp_toy_data_dir) -> Path:
-    filepath = temp_toy_data_dir / "test_3dims_3vars_4coords_1group_part1.nc"
+def ds_3dims_3vars_2coords_nogroup(temp_toy_data_dir) -> Path:
+    filepath = temp_toy_data_dir / "test_3dims_3vars_2coords_nogroup.nc"
+
+    f = nc.Dataset(filename=filepath, mode="w")
+    f = add_to_ds_3dims_3vars_2coords_nogroup(f, step_values=[9, 10, 11])
+    f.close()
+
+    return filepath
+
+
+@pytest.fixture(scope="function")
+def ds_3dims_3vars_2coords_nogroup_duplicate_dimensions(temp_toy_data_dir) -> Path:
+    filepath = temp_toy_data_dir / "test_3dims_3vars_2coords_nogroup_duplicate_dimensions.nc"
+
+    f = nc.Dataset(filename=filepath, mode="w")
+    f = add_to_ds_3dims_3vars_2coords_nogroup_duplicate_dimensions(f, step_values=[9, 10, 11])
+    f.close()
+
+    return filepath
+
+
+@pytest.fixture(scope="function")
+def ds_3dims_3vars_3coords_1group_part1(temp_toy_data_dir) -> Path:
+    filepath = temp_toy_data_dir / "test_3dims_3vars_3coords_1group_part1.nc"
 
     f = nc.Dataset(filename=filepath, mode="w")
-    f = add_to_ds_3dims_3vars_4coords_1group_with_step_values(f, step_values=[9, 10, 11])
+    f = add_to_ds_3dims_3vars_3coords_1group_with_step_values(f, step_values=[9, 10, 11])
     f.close()
 
     return filepath
 
 
 @pytest.fixture(scope="function")
-def ds_3dims_3vars_4coords_1group_part2(temp_toy_data_dir):
-    filepath = temp_toy_data_dir / "test_3dims_3vars_4coords_1group_part2.nc"
+def ds_3dims_3vars_3coords_1group_part2(temp_toy_data_dir):
+    filepath = temp_toy_data_dir / "test_3dims_3vars_3coords_1group_part2.nc"
 
     f = nc.Dataset(filename=filepath, mode="w")
-    f = add_to_ds_3dims_3vars_4coords_1group_with_step_values(f, step_values=[12, 13, 14])
+    f = add_to_ds_3dims_3vars_3coords_1group_with_step_values(f, step_values=[12, 13, 14])
     f.close()
 
     return filepath
 
 
 @pytest.fixture(scope="function")
-def ds_3dims_3vars_4coords_1group_part3(temp_toy_data_dir):
-    filepath = temp_toy_data_dir / "test_3dims_3vars_4coords_1group_part3.nc"
+def ds_3dims_3vars_3coords_1group_part3(temp_toy_data_dir):
+    filepath = temp_toy_data_dir / "test_3dims_3vars_3coords_1group_part3.nc"
 
     f = nc.Dataset(filename=filepath, mode="w")
-    f = add_to_ds_3dims_3vars_4coords_1group_with_step_values(f, step_values=[6, 7, 8])
+    f = add_to_ds_3dims_3vars_3coords_1group_with_step_values(f, step_values=[6, 7, 8])
     f.close()
 
     return filepath
diff --git a/tests/unit/test_dataset_and_group_handling.py b/tests/unit/test_dataset_and_group_handling.py
index 5c50951..70a98b3 100644
--- a/tests/unit/test_dataset_and_group_handling.py
+++ b/tests/unit/test_dataset_and_group_handling.py
@@ -42,29 +42,29 @@ def test_toy_dataset_with_singleton_null_values_is_identified_as_empty(
 
 
 def test_dataset_with_values_is_identified_as_not_empty(
-    ds_3dims_3vars_4coords_1group_part1,
+    ds_3dims_3vars_3coords_1group_part1,
 ):
     """Ensure that a dataset with non-null arrays is identified as NOT empty."""
-    with nc.Dataset(ds_3dims_3vars_4coords_1group_part1) as ds:
+    with nc.Dataset(ds_3dims_3vars_3coords_1group_part1) as ds:
         assert _is_file_empty(ds) is False
 
 
-def test_get_nested_group(ds_3dims_3vars_4coords_1group_part1):
+def test_get_nested_group(ds_3dims_3vars_3coords_1group_part1):
     """Ensure that the retrieved group is correct."""
-    with nc.Dataset(ds_3dims_3vars_4coords_1group_part1) as ds:
+    with nc.Dataset(ds_3dims_3vars_3coords_1group_part1) as ds:
         group_obj = _get_nested_group(ds, "__Group1__level")
         assert isinstance(group_obj, nc.Group)
 
 
-def test_get_root_group(ds_3dims_3vars_4coords_1group_part1):
+def test_get_root_group(ds_3dims_3vars_3coords_1group_part1):
     """Ensure that the retrieved group is correct."""
-    with nc.Dataset(ds_3dims_3vars_4coords_1group_part1) as ds:
+    with nc.Dataset(ds_3dims_3vars_3coords_1group_part1) as ds:
         group_obj = _get_nested_group(ds, "__track")
         assert group_obj == ds
 
 
-def test_get_root_group_when_no_delimiter_present(ds_3dims_3vars_4coords_1group_part1):
+def test_get_root_group_when_no_delimiter_present(ds_3dims_3vars_3coords_1group_part1):
     """Ensure that the retrieved group is correct."""
-    with nc.Dataset(ds_3dims_3vars_4coords_1group_part1) as ds:
+    with nc.Dataset(ds_3dims_3vars_3coords_1group_part1) as ds:
         group_obj = _get_nested_group(ds, "track")
         assert group_obj == ds
diff --git a/tests/unit/test_dimension_cleanup.py b/tests/unit/test_dimension_cleanup.py
new file mode 100644
index 0000000..c05c1cc
--- /dev/null
+++ b/tests/unit/test_dimension_cleanup.py
@@ -0,0 +1,29 @@
+"""Tests for netCDF dimension clean up operations."""
+
+# pylint: disable=C0116, C0301
+
+import netCDF4 as nc
+
+from concatenator.dimension_cleanup import (
+    get_attributes_minus_fillvalue_and_renamed_coords,
+)
+
+
+def test_get_attributes_minus_fillvalue_and_renamed_coords(ds_3dims_3vars_2coords_nogroup):
+    with nc.Dataset(ds_3dims_3vars_2coords_nogroup, "r+") as ds:
+        attr_contents_dict = get_attributes_minus_fillvalue_and_renamed_coords(
+            original_var_name="var0", new_var_name="new_dim", original_dataset=ds
+        )
+
+        assert attr_contents_dict["coordinates"] == "new_dim track"
+
+
+# TODO: this next test is still failing.
+#  Should go away once using xarray's DataTree instead of flattening group structure.
+# def test_remove_duplicate_dims(ds_3dims_3vars_2coords_nogroup_duplicate_dimensions):
+#     with nc.Dataset(ds_3dims_3vars_2coords_nogroup_duplicate_dimensions, "r+") as ds:
+#         ds_with_replaced_dims = remove_duplicate_dims(ds)
+#
+#         ds_with_replaced_dims["var0"].coordinates = "var0 track track"
+#
+#         assert ds_with_replaced_dims["var0"].coordinates == "var0 track track_1"

From 79ab5c2a617b294ac14920e6e92fad22238acee2 Mon Sep 17 00:00:00 2001
From: Daniel Kaufman <114174502+danielfromearth@users.noreply.github.com>
Date: Tue, 19 Nov 2024 11:59:39 -0500
Subject: [PATCH 14/37] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5496df0..fd48205 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file.
 The format is based on [Common Changelog](https://common-changelog.org/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## Unreleased
+## [1.6.0] - 2024-11-19
 
 ### Changed
 

From a1b7884c3cc3a2d3ddc5254ba289343bbeeecddb Mon Sep 17 00:00:00 2001
From: stitchee bot <stitchee@noreply.github.com>
Date: Tue, 19 Nov 2024 17:01:32 +0000
Subject: [PATCH 15/37] /version 1.6.0rc2

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 02e4ef1..9a8186f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "stitchee"
-version = "1.6.0rc1"
+version = "1.6.0rc2"
 description = "NetCDF4 Along-existing-dimension Concatenation Service"
 authors = ["Daniel Kaufman <daniel.kaufman@nasa.gov>"]
 readme = "README.md"

From 621ed4900e1f14a706b1bf2a6c32ba3a34304273 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Tue, 19 Nov 2024 12:26:28 -0500
Subject: [PATCH 16/37] use alias dataset.sizes because of the xarray
 FutureWarning:

The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`
---
 concatenator/dataset_and_group_handling.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/concatenator/dataset_and_group_handling.py b/concatenator/dataset_and_group_handling.py
index d387137..281c09c 100644
--- a/concatenator/dataset_and_group_handling.py
+++ b/concatenator/dataset_and_group_handling.py
@@ -195,7 +195,7 @@ def regroup_flattened_dataset(
         for dim_name, _ in dataset.dims.items():
             new_dim_name = str(dim_name).rsplit(concatenator.group_delim, 1)[-1]
             dim_group = _get_nested_group(base_dataset, str(dim_name))
-            dim_group.createDimension(new_dim_name, dataset.dims[dim_name])
+            dim_group.createDimension(new_dim_name, dataset.sizes[dim_name])
             # dst.createDimension(
             #     name, (len(dimension) if not dimension.isunlimited() else None))
 

From 9356d788e6384b80dd6241272655f4cc20606624 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Tue, 19 Nov 2024 12:27:48 -0500
Subject: [PATCH 17/37] fix updated fixture name

---
 tests/integration/test_history_construction.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/integration/test_history_construction.py b/tests/integration/test_history_construction.py
index 04e5f88..36dae30 100644
--- a/tests/integration/test_history_construction.py
+++ b/tests/integration/test_history_construction.py
@@ -10,8 +10,8 @@
 def test_construct_and_append_history_for_sample_concatenation(
     temp_toy_data_dir,
     temp_output_dir,
-    ds_3dims_3vars_4coords_1group_part1,
-    ds_3dims_3vars_4coords_1group_part2,
+    ds_3dims_3vars_3coords_1group_part1,
+    ds_3dims_3vars_3coords_1group_part2,
 ):
     output_path = str(temp_output_dir.joinpath("simple_sample_concatenated.nc"))  # type: ignore
     prepared_input_files = prep_input_files(temp_toy_data_dir, temp_output_dir)

From 2e38bb3415557a66ddb9c859287f1277084d540c Mon Sep 17 00:00:00 2001
From: stitchee bot <stitchee@noreply.github.com>
Date: Tue, 19 Nov 2024 17:29:49 +0000
Subject: [PATCH 18/37] /version 1.6.0rc3

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9a8186f..1a98e90 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "stitchee"
-version = "1.6.0rc2"
+version = "1.6.0rc3"
 description = "NetCDF4 Along-existing-dimension Concatenation Service"
 authors = ["Daniel Kaufman <daniel.kaufman@nasa.gov>"]
 readme = "README.md"

From 5f906c9288638cd66948012eb16db1a0e736c751 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Tue, 19 Nov 2024 13:28:51 -0500
Subject: [PATCH 19/37] add unit tests for input and output path validation
 functions

---
 tests/unit/test_file_ops.py | 30 +++++++++++++++++++++++++++++-
 1 file changed, 29 insertions(+), 1 deletion(-)

diff --git a/tests/unit/test_file_ops.py b/tests/unit/test_file_ops.py
index 8044e0f..020975d 100644
--- a/tests/unit/test_file_ops.py
+++ b/tests/unit/test_file_ops.py
@@ -1,6 +1,10 @@
 from pathlib import Path
 
-from concatenator.file_ops import add_label_to_path
+import pytest
+
+from concatenator.file_ops import add_label_to_path, validate_input_path, validate_output_path
+
+from .. import data_for_tests_dir
 
 
 def test_add_label_to_path():
@@ -10,3 +14,27 @@ def test_add_label_to_path():
     new_path = str((this_module_dir / "tests_file_new-suffix.nc").resolve())
 
     assert add_label_to_path(origin_path, label="_new-suffix") == new_path
+
+
+def test_validate_bad_output_paths():
+    path_to_file_that_exists = str(
+        data_for_tests_dir / "unit-test-data" / "TEMPO_NO2_L2_V03_20240328T154353Z_S008G01.nc4"
+    )
+
+    with pytest.raises(FileExistsError):
+        validate_output_path(path_to_file_that_exists, overwrite=False)
+
+    with pytest.raises(TypeError):
+        validate_output_path(str(data_for_tests_dir), overwrite=False)
+
+
+def test_validate_bad_non_existent_input_path():
+    path_to_file_that_does_not_exist = str(
+        data_for_tests_dir / "unit-test-data" / "non-existent.nc4"
+    )
+
+    with pytest.raises(TypeError):
+        validate_input_path([path_to_file_that_does_not_exist])
+
+    with pytest.raises(TypeError):
+        validate_input_path([])

From ef88af86108fc87f601f0abd01ecde226fa7d37c Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Tue, 19 Nov 2024 13:34:32 -0500
Subject: [PATCH 20/37] remove inadvertent comments

---
 .../test_concat_with_subsetting_first.py      | 64 -------------------
 1 file changed, 64 deletions(-)

diff --git a/tests/integration/test_concat_with_subsetting_first.py b/tests/integration/test_concat_with_subsetting_first.py
index c46b2a3..a045224 100644
--- a/tests/integration/test_concat_with_subsetting_first.py
+++ b/tests/integration/test_concat_with_subsetting_first.py
@@ -37,70 +37,6 @@ def test_concat_with_subsetting_first(temp_output_dir):
         file_names,
         output_file=str(
             (temp_output_dir / "output_harmony_subsetting_to_stitchee_test.nc").resolve()
-            #         ),
-            #         concat_dim="mirror_step",
-            #         concat_method="xarray-concat",
-            #         write_tmp_flat_concatenated=True,
-            #         keep_tmp_files=True,
-            #     )
-            #
-            #     assert output_path
-            #
-            # C1262899916-LARC_CLOUD
-            #
-            # G1269044803-LARC_CLOUD
-            # G1269044708-LARC_CLOUD
-            # G1269044681-LARC_CLOUD
-            # G1269044688-LARC_CLOUD
-            # G1269044514-LARC_CLOUD
-            # G1269044741-LARC_CLOUD
-            # G1269044710-LARC_CLOUD
-            # G1269044439-LARC_CLOUD
-            # G1269044715-LARC_CLOUD
-            # G1269044815-LARC_CLOUD
-            # G1269044726-LARC_CLOUD
-            # G1269044787-LARC_CLOUD
-            # G1269044827-LARC_CLOUD
-            # G1269044658-LARC_CLOUD
-            # G1269044679-LARC_CLOUD
-            # G1269044727-LARC_CLOUD
-            # subset=lat(32.56485%3A42.82943)&
-            # subset=lon(-135.7248%3A-52.76692)&
-            # subset=time(%222024-08-02T00%3A00%3A00.000Z%22%3A%222024-08-02T10%3A39%3A37.000Z%22)&
-            # concatenate=true&skipPreview=true
-            #
-            # def test_concat_with_subsetting_first(temp_output_dir):
-            #     """Subsets 4 granules from the TEMPO NO2 collection, and then concatenates them."""
-            #     harmony_client = Client()
-            #
-            #     # "Nitrogen Dioxide total column"
-            #     request = Request(
-            #         collection=Collection(id="C2930725014-LARC_CLOUD"),
-            #         temporal={
-            #             "start": dt.datetime(2024, 5, 13, 11, 0, 0),
-            #             "stop": dt.datetime(2024, 5, 13, 20, 0, 0),
-            #         },
-            #         spatial=BBox(-130, 30, -115, 35),
-            #         concatenate=False,
-            #     )
-            #     if not request.is_valid():
-            #         raise RuntimeError
-            #
-            #     # Submit and wait for job to complete.
-            #     job_id = harmony_client.submit(request)
-            #     print(f"Job ID: {job_id}")
-            #     harmony_client.wait_for_processing(job_id, show_progress=False)
-            #
-            #     # Download the result files.
-            #     futures = harmony_client.download_all(job_id, directory=str(temp_output_dir))
-            #     file_names = [f.result() for f in futures]
-            #     print(f"File names: {file_names}")
-            #
-            #     # Try concatenating the resulting files
-            #     output_path = stitchee(
-            #         file_names,
-            #         output_file=str(
-            #             (temp_output_dir / "output_harmony_subsetting_to_stitchee_test.nc").resolve()
         ),
         concat_dim="mirror_step",
         concat_method="xarray-concat",

From 65da7f7de30589526331704aa9bce943f26dca19 Mon Sep 17 00:00:00 2001
From: Daniel Kaufman <114174502+danielfromearth@users.noreply.github.com>
Date: Tue, 19 Nov 2024 13:37:45 -0500
Subject: [PATCH 21/37] revert back to 1.6.0 rc version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index b95b68e..1a98e90 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "stitchee"
-version = "1.7.0a0"
+version = "1.6.0rc3"
 description = "NetCDF4 Along-existing-dimension Concatenation Service"
 authors = ["Daniel Kaufman <daniel.kaufman@nasa.gov>"]
 readme = "README.md"

From ef5bc93d0c06a8374ad3b9ddeeb981fd80b2fa54 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Tue, 19 Nov 2024 13:44:31 -0500
Subject: [PATCH 22/37] update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fd48205..8eba1ea 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - update pre-commit: to autoupdate and with gitleaks ([#247](https://github.com/nasa/stitchee/pull/247))([**@danielfromearth**](https://github.com/danielfromearth))
+- improved test coverage ([#248](https://github.com/nasa/stitchee/pull/248))([**@danielfromearth**](https://github.com/danielfromearth))
 
 ## [1.5.0] - 2024-11-08
 

From 839563e47edb0e2e943d18e09ce34fa8010d97a6 Mon Sep 17 00:00:00 2001
From: stitchee bot <stitchee@noreply.github.com>
Date: Tue, 19 Nov 2024 18:53:34 +0000
Subject: [PATCH 23/37] /version 1.6.0rc4

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 1a98e90..3a9dd9b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "stitchee"
-version = "1.6.0rc3"
+version = "1.6.0rc4"
 description = "NetCDF4 Along-existing-dimension Concatenation Service"
 authors = ["Daniel Kaufman <daniel.kaufman@nasa.gov>"]
 readme = "README.md"

From 5dc16f5d075a1f5248d7c078e4fc34a0735d705b Mon Sep 17 00:00:00 2001
From: Daniel Kaufman <114174502+danielfromearth@users.noreply.github.com>
Date: Tue, 19 Nov 2024 14:04:02 -0500
Subject: [PATCH 24/37] skip pre-commit when committing version bump

---
 .github/workflows/build-pipeline.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-pipeline.yml b/.github/workflows/build-pipeline.yml
index 04bed58..c16f32c 100644
--- a/.github/workflows/build-pipeline.yml
+++ b/.github/workflows/build-pipeline.yml
@@ -121,7 +121,7 @@ jobs:
         run: |
           git config --global user.name 'stitchee bot'
           git config --global user.email 'stitchee@noreply.github.com'
-          git commit -am "/version ${{ env.software_version }}"
+          git commit -am "/version ${{ env.software_version }}" --no-verify
           git push
 
       # Builds and pushes the package to the Python Package Index (PyPI)

From d22521d6ae832e723a9adca28d129ff611602705 Mon Sep 17 00:00:00 2001
From: stitchee bot <stitchee@noreply.github.com>
Date: Tue, 19 Nov 2024 19:05:52 +0000
Subject: [PATCH 25/37] /version 1.6.0rc5

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3a9dd9b..640710c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "stitchee"
-version = "1.6.0rc4"
+version = "1.6.0rc5"
 description = "NetCDF4 Along-existing-dimension Concatenation Service"
 authors = ["Daniel Kaufman <daniel.kaufman@nasa.gov>"]
 readme = "README.md"

From 567d7b6ba026a694b7b70d6ba04b069bf68d441a Mon Sep 17 00:00:00 2001
From: stitchee bot <stitchee@noreply.github.com>
Date: Tue, 19 Nov 2024 19:15:59 +0000
Subject: [PATCH 26/37] /version 1.6.0

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 640710c..2fcabb5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "stitchee"
-version = "1.6.0rc5"
+version = "1.6.0"
 description = "NetCDF4 Along-existing-dimension Concatenation Service"
 authors = ["Daniel Kaufman <daniel.kaufman@nasa.gov>"]
 readme = "README.md"

From 764aee24b05915c36312c9f5829a5c12eadccadd Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Tue, 19 Nov 2024 15:59:47 -0500
Subject: [PATCH 27/37] version 1.7.0a1

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2fcabb5..25834c4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "stitchee"
-version = "1.6.0"
+version = "1.7.0a1"
 description = "NetCDF4 Along-existing-dimension Concatenation Service"
 authors = ["Daniel Kaufman <daniel.kaufman@nasa.gov>"]
 readme = "README.md"

From a4c895f657e8af1015d8c4eeb674e8a56e908fb9 Mon Sep 17 00:00:00 2001
From: stitchee bot <stitchee@noreply.github.com>
Date: Tue, 19 Nov 2024 21:01:41 +0000
Subject: [PATCH 28/37] /version 1.7.0a2

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 25834c4..116c30a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "stitchee"
-version = "1.7.0a1"
+version = "1.7.0a2"
 description = "NetCDF4 Along-existing-dimension Concatenation Service"
 authors = ["Daniel Kaufman <daniel.kaufman@nasa.gov>"]
 readme = "README.md"

From 3e9399e6660875b118a385e05fbedbe02d551fee Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 22 Nov 2024 22:20:19 +0000
Subject: [PATCH 29/37] Bump tornado from 6.4.1 to 6.4.2

Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.4.1 to 6.4.2.
- [Changelog](https://github.com/tornadoweb/tornado/blob/v6.4.2/docs/releases.rst)
- [Commits](https://github.com/tornadoweb/tornado/compare/v6.4.1...v6.4.2)

---
updated-dependencies:
- dependency-name: tornado
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 poetry.lock | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 9283504..aa66d69 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
 
 [[package]]
 name = "appnope"
@@ -2749,22 +2749,22 @@ files = [
 
 [[package]]
 name = "tornado"
-version = "6.4.1"
+version = "6.4.2"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "tornado-6.4.1-cp38-abi3-macosx_10_9_universal2.whl", hash = "sha256:163b0aafc8e23d8cdc3c9dfb24c5368af84a81e3364745ccb4427669bf84aec8"},
-    {file = "tornado-6.4.1-cp38-abi3-macosx_10_9_x86_64.whl", hash = "sha256:6d5ce3437e18a2b66fbadb183c1d3364fb03f2be71299e7d10dbeeb69f4b2a14"},
-    {file = "tornado-6.4.1-cp38-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e2e20b9113cd7293f164dc46fffb13535266e713cdb87bd2d15ddb336e96cfc4"},
-    {file = "tornado-6.4.1-cp38-abi3-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:8ae50a504a740365267b2a8d1a90c9fbc86b780a39170feca9bcc1787ff80842"},
-    {file = "tornado-6.4.1-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:613bf4ddf5c7a95509218b149b555621497a6cc0d46ac341b30bd9ec19eac7f3"},
-    {file = "tornado-6.4.1-cp38-abi3-musllinux_1_2_aarch64.whl", hash = "sha256:25486eb223babe3eed4b8aecbac33b37e3dd6d776bc730ca14e1bf93888b979f"},
-    {file = "tornado-6.4.1-cp38-abi3-musllinux_1_2_i686.whl", hash = "sha256:454db8a7ecfcf2ff6042dde58404164d969b6f5d58b926da15e6b23817950fc4"},
-    {file = "tornado-6.4.1-cp38-abi3-musllinux_1_2_x86_64.whl", hash = "sha256:a02a08cc7a9314b006f653ce40483b9b3c12cda222d6a46d4ac63bb6c9057698"},
-    {file = "tornado-6.4.1-cp38-abi3-win32.whl", hash = "sha256:d9a566c40b89757c9aa8e6f032bcdb8ca8795d7c1a9762910c722b1635c9de4d"},
-    {file = "tornado-6.4.1-cp38-abi3-win_amd64.whl", hash = "sha256:b24b8982ed444378d7f21d563f4180a2de31ced9d8d84443907a0a64da2072e7"},
-    {file = "tornado-6.4.1.tar.gz", hash = "sha256:92d3ab53183d8c50f8204a51e6f91d18a15d5ef261e84d452800d4ff6fc504e9"},
+    {file = "tornado-6.4.2-cp38-abi3-macosx_10_9_universal2.whl", hash = "sha256:e828cce1123e9e44ae2a50a9de3055497ab1d0aeb440c5ac23064d9e44880da1"},
+    {file = "tornado-6.4.2-cp38-abi3-macosx_10_9_x86_64.whl", hash = "sha256:072ce12ada169c5b00b7d92a99ba089447ccc993ea2143c9ede887e0937aa803"},
+    {file = "tornado-6.4.2-cp38-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1a017d239bd1bb0919f72af256a970624241f070496635784d9bf0db640d3fec"},
+    {file = "tornado-6.4.2-cp38-abi3-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:c36e62ce8f63409301537222faffcef7dfc5284f27eec227389f2ad11b09d946"},
+    {file = "tornado-6.4.2-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bca9eb02196e789c9cb5c3c7c0f04fb447dc2adffd95265b2c7223a8a615ccbf"},
+    {file = "tornado-6.4.2-cp38-abi3-musllinux_1_2_aarch64.whl", hash = "sha256:304463bd0772442ff4d0f5149c6f1c2135a1fae045adf070821c6cdc76980634"},
+    {file = "tornado-6.4.2-cp38-abi3-musllinux_1_2_i686.whl", hash = "sha256:c82c46813ba483a385ab2a99caeaedf92585a1f90defb5693351fa7e4ea0bf73"},
+    {file = "tornado-6.4.2-cp38-abi3-musllinux_1_2_x86_64.whl", hash = "sha256:932d195ca9015956fa502c6b56af9eb06106140d844a335590c1ec7f5277d10c"},
+    {file = "tornado-6.4.2-cp38-abi3-win32.whl", hash = "sha256:2876cef82e6c5978fde1e0d5b1f919d756968d5b4282418f3146b79b58556482"},
+    {file = "tornado-6.4.2-cp38-abi3-win_amd64.whl", hash = "sha256:908b71bf3ff37d81073356a5fadcc660eb10c1476ee6e2725588626ce7e5ca38"},
+    {file = "tornado-6.4.2.tar.gz", hash = "sha256:92bad5b4746e9879fd7bf1eb21dce4e3fc5128d71601f80005afa39237ad620b"},
 ]
 
 [[package]]

From 2e2dba0f04260c7af93f5e94fed8e3557ab3b2ab Mon Sep 17 00:00:00 2001
From: stitchee bot <stitchee@noreply.github.com>
Date: Mon, 25 Nov 2024 14:42:19 +0000
Subject: [PATCH 30/37] /version 1.7.0a3

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 116c30a..459dd2d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "stitchee"
-version = "1.7.0a2"
+version = "1.7.0a3"
 description = "NetCDF4 Along-existing-dimension Concatenation Service"
 authors = ["Daniel Kaufman <daniel.kaufman@nasa.gov>"]
 readme = "README.md"

From 53ca35ef4af53d57af245da4c0a23a7b5997336d Mon Sep 17 00:00:00 2001
From: Andrey Kim <andrey.kim@nasa.gov>
Date: Wed, 27 Nov 2024 08:20:45 -0500
Subject: [PATCH 31/37] prevent xarray from changing variable types on
 open_dataset

---
 concatenator/stitchee.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/concatenator/stitchee.py b/concatenator/stitchee.py
index 9da96f4..7535bf0 100644
--- a/concatenator/stitchee.py
+++ b/concatenator/stitchee.py
@@ -150,6 +150,7 @@ def stitchee(
                     decode_times=False,
                     decode_coords=False,
                     drop_variables=coord_vars,
+                    mask_and_scale=False
                 )
 
                 # Determine value for later dataset sorting.

From 1f52006d9f9b63504e4679bfc742bf31683e10d4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 27 Nov 2024 14:08:43 +0000
Subject: [PATCH 32/37] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 concatenator/stitchee.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/concatenator/stitchee.py b/concatenator/stitchee.py
index 7535bf0..70a833d 100644
--- a/concatenator/stitchee.py
+++ b/concatenator/stitchee.py
@@ -150,7 +150,7 @@ def stitchee(
                     decode_times=False,
                     decode_coords=False,
                     drop_variables=coord_vars,
-                    mask_and_scale=False
+                    mask_and_scale=False,
                 )
 
                 # Determine value for later dataset sorting.

From 60b6e1703fefd19bc077b8c76823044ec5bddf1e Mon Sep 17 00:00:00 2001
From: stitchee bot <stitchee@noreply.github.com>
Date: Wed, 27 Nov 2024 14:15:56 +0000
Subject: [PATCH 33/37] /version 1.7.0a4

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 459dd2d..d01d752 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "stitchee"
-version = "1.7.0a3"
+version = "1.7.0a4"
 description = "NetCDF4 Along-existing-dimension Concatenation Service"
 authors = ["Daniel Kaufman <daniel.kaufman@nasa.gov>"]
 readme = "README.md"

From f4546d34484ef192d75c5f1b4deb605fafc539eb Mon Sep 17 00:00:00 2001
From: stitchee bot <stitchee@noreply.github.com>
Date: Wed, 27 Nov 2024 14:23:18 +0000
Subject: [PATCH 34/37] /version 1.6.1rc1

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index d01d752..307cb6d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "stitchee"
-version = "1.7.0a4"
+version = "1.6.1rc1"
 description = "NetCDF4 Along-existing-dimension Concatenation Service"
 authors = ["Daniel Kaufman <daniel.kaufman@nasa.gov>"]
 readme = "README.md"

From 164b254f4711e98366b05e8e89adc56e56f54e01 Mon Sep 17 00:00:00 2001
From: Daniel Kaufman <114174502+danielfromearth@users.noreply.github.com>
Date: Wed, 27 Nov 2024 10:17:24 -0500
Subject: [PATCH 35/37] Update CHANGELOG.md

---
 CHANGELOG.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8eba1ea..4524a7f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Common Changelog](https://common-changelog.org/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.6.1] - 2024-11-27
+
+### Fixed
+
+- prevent xarray from changing variable types on open_dataset ([#254](https://github.com/nasa/stitchee/pull/254))([**@ank1m**](https://github.com/ank1m))
+
 ## [1.6.0] - 2024-11-19
 
 ### Changed

From fc8afb51235342f8272ee78deabf441a3eeb6a9a Mon Sep 17 00:00:00 2001
From: stitchee bot <stitchee@noreply.github.com>
Date: Wed, 27 Nov 2024 15:19:21 +0000
Subject: [PATCH 36/37] /version 1.6.1rc2

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 307cb6d..b387c4c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "stitchee"
-version = "1.6.1rc1"
+version = "1.6.1rc2"
 description = "NetCDF4 Along-existing-dimension Concatenation Service"
 authors = ["Daniel Kaufman <daniel.kaufman@nasa.gov>"]
 readme = "README.md"

From fd35e871f4adeccd7529ce8b003389ff19d0edd7 Mon Sep 17 00:00:00 2001
From: stitchee bot <stitchee@noreply.github.com>
Date: Wed, 27 Nov 2024 15:27:31 +0000
Subject: [PATCH 37/37] /version 1.6.1

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index b387c4c..18aeaa8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "stitchee"
-version = "1.6.1rc2"
+version = "1.6.1"
 description = "NetCDF4 Along-existing-dimension Concatenation Service"
 authors = ["Daniel Kaufman <daniel.kaufman@nasa.gov>"]
 readme = "README.md"