podaac-l2ss-py 3.3.3__tar.gz

podaac_l2ss_py-3.3.3/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright 2025 California Institute of Technology
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

podaac_l2ss_py-3.3.3/PKG-INFO

@@ -0,0 +1,163 @@
+Metadata-Version: 2.4
+Name: podaac-l2ss-py
+Version: 3.3.3
+Summary: L2 Subsetter Service
+License: Apache-2.0
+License-File: LICENSE
+Author: podaac-tva
+Author-email: podaac-tva@jpl.nasa.gov
+Requires-Python: >=3.12,<4.0
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Provides-Extra: harmony
+Requires-Dist: Shapely (>=2.0.6,<3.0.0)
+Requires-Dist: cf-xarray
+Requires-Dist: geopandas (>=1.0.1,<2.0.0)
+Requires-Dist: h5py (>=3.6.0,<4.0.0)
+Requires-Dist: harmony-service-lib (>=3.0.0,<4.0.0) ; extra == "harmony"
+Requires-Dist: importlib-metadata (>=9.0.0,<10.0.0)
+Requires-Dist: julian (>=0.14,<0.15)
+Requires-Dist: netCDF4 (>=1.5,<2.0)
+Requires-Dist: numpy (>=2.2.4,<3.0.0)
+Requires-Dist: pandas (==2.3.3)
+Requires-Dist: pystac (>=1.10.1,<2.0.0) ; extra == "harmony"
+Requires-Dist: xarray[parallel] (<=2025.1.0)
+Project-URL: Repository, https://github.com/podaac/l2ss-py
+Description-Content-Type: text/markdown
+
+# l2ss-py
+
+[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=podaac_l2ss-py&metric=coverage)](https://sonarcloud.io/dashboard?id=podaac_l2ss-py)  
+develop: [![Develop Build](https://github.com/podaac/l2ss-py/actions/workflows/build-pipeline.yml/badge.svg?branch=develop&event=push)](https://github.com/podaac/l2ss-py/actions/workflows/build-pipeline.yml)  
+main: [![Main Build](https://github.com/podaac/l2ss-py/actions/workflows/build-pipeline.yml/badge.svg?branch=main&event=push)](https://github.com/podaac/l2ss-py/actions/workflows/build-pipeline.yml)
+
+Harmony service for subsetting L2 data. l2ss-py supports:
+
+- Spatial subsetting
+    - Bounding box
+    - Shapefile subsetting
+    - GeoJSON subsetting
+- Temporal subsetting
+- Variable subsetting
+- Vertical subsetting
+
+If you would like to contribute to l2ss-py, refer to the [contribution document](CONTRIBUTING.md).
+
+## Initial setup, with poetry
+
+1. Follow the instructions for installing `poetry` [here](https://python-poetry.org/docs/).
+2. Install l2ss-py, with its dependencies, by running the following from the repository directory:
+
+```
+poetry install
+```
+
+***Note:*** l2ss-py can be installed as above and run without any dependency on `harmony`. 
+However, to additionally test the harmony adapter layer, 
+extra dependencies can be installed with `poetry install -E harmony`.
+
+## How to test l2ss-py locally
+
+### Unit tests
+
+There are comprehensive unit tests for l2ss-py. The tests can be run as follows:
+
+```
+poetry run pytest -m "not aws and not integration" tests/
+```
+
+You can generate coverage reports as follows:
+
+```
+poetry run pytest --junitxml=build/reports/pytest.xml --cov=podaac/ --cov-report=html -m "not aws and not integration" tests/
+```
+
+***Note:*** The majority of the tests execute core functionality of l2ss-py without ever interacting with the harmony python modules. 
+The `test_subset_harmony` tests, however, are explicitly for testing the harmony adapter layer 
+and do require the harmony optional dependencies be installed, 
+as described above with the `-E harmony` argument.
+
+### l2ss-py script
+
+You can run l2ss-py on a single granule without using Harmony. In order 
+to run this, the l2ss-py package must be installed in your current 
+Python interpreter
+
+```
+$ l2ss-py --help
+usage: l2ss-py [-h] [--bbox BBOX BBOX BBOX BBOX] [--variables VARIABLES [VARIABLES ...]] [--min-time MIN_TIME] [--max-time MAX_TIME] [--cut] [--shapefile SHAPEFILE] [--pixel_subset] [--vertical-var VERTICAL_VAR] [--vertical-min VERTICAL_MIN] [--vertical-max VERTICAL_MAX]
+               input_file output_file
+
+Run l2ss-py
+
+positional arguments:
+  input_file            File to subset
+  output_file           Output file
+
+options:
+  -h, --help            show this help message and exit
+  --bbox BBOX BBOX BBOX BBOX
+                        Bounding box in the form min_lon min_lat max_lon max_lat
+  --variables VARIABLES [VARIABLES ...]
+                        Variables, only include if variable subset is desired. Should be a space separated list of variable names e.g. sst wind_dir sst_error ...
+  --min-time MIN_TIME   Min time. Should be ISO-8601 format. Only include if temporal subset is desired.
+  --max-time MAX_TIME   Max time. Should be ISO-8601 format. Only include if temporal subset is desired.
+  --cut                 If provided, scanline will be cut
+  --shapefile SHAPEFILE
+                        Path to either shapefile or geojson file used to subset the provided input granule
+  --pixel_subset        To pixel cut based the lon lat on the bounding box
+  --vertical-var VERTICAL_VAR
+                        Name of the vertical variable to subset by (e.g., depth, altitude)
+  --vertical-min VERTICAL_MIN
+                        Minimum value for vertical subsetting (inclusive)
+  --vertical-max VERTICAL_MAX
+                        Maximum value for vertical subsetting (inclusive)
+```
+
+#### Additional subsetting options
+
+The following options are also recorded in the output file's metadata history for provenance and reproducibility:
+- `--min-time` and `--max-time` (temporal subsetting)
+- `--variables` (variable subsetting)
+- `--vertical-var`, `--vertical-min`, `--vertical-max` (vertical subsetting)
+- `--cut`, `--pixel_subset`, `--shapefile`, and `--bbox` (spatial subsetting)
+
+All subsetting parameters used in a run are included in the output file's `history` and `history_json` attributes.
+
+For example:
+
+```
+l2ss-py /path/to/input.nc /path/to/output.nc --bbox -50 -10 50 10 --variables wind_speed wind_dir ice_age time --min-time '2015-07-02T09:00:00' --max-time '2015-07-02T10:00:00' --cut --vertical-var depth --vertical-min 0 --vertical-max 100
+```
+
+An addition to providing a bounding box, spatial subsetting can be achieved by passing in a shapefile or a geojson file. 
+
+```shell script
+poetry run l2ss-py /path/to/input.nc /path/to/output.nc --shapefile /path/to/test.shp
+```
+
+or 
+
+```shell script
+poetry run l2ss-py /path/to/input.nc /path/to/output.nc --shapefile /path/to/test.geojson
+```
+
+### Running Harmony locally
+
+In order to fully test l2ss-py with Harmony, you can run Harmony locally. This requires the data exists in UAT Earthdata Cloud.
+
+1. Set up local Harmony instance. Instructions [here](https://github.com/nasa/harmony#Quick-Start)
+2. Add concept ID for your data to [services.yml](https://github.com/nasa/harmony/blob/main/config/services.yml)
+3. Execute a local Harmony l2ss-py request. For example:
+    ```
+   localhost:3000/YOUR_COLLECTION_ID/ogc-api-coverages/1.0.0/collections/all/coverage/rangeset?format=application%2Fx-netcdf4&subset=lat(-10%3A10)&subset=lon(-10%3A10)&maxResults=2
+   ```
+
+## NASA EOSDIS Integration
+
+Detailed instructions for integrating with EOSDIS can be found [here](EOSDISIntegrations.md).
+

podaac_l2ss_py-3.3.3/README.md

@@ -0,0 +1,131 @@
+# l2ss-py
+
+[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=podaac_l2ss-py&metric=coverage)](https://sonarcloud.io/dashboard?id=podaac_l2ss-py)  
+develop: [![Develop Build](https://github.com/podaac/l2ss-py/actions/workflows/build-pipeline.yml/badge.svg?branch=develop&event=push)](https://github.com/podaac/l2ss-py/actions/workflows/build-pipeline.yml)  
+main: [![Main Build](https://github.com/podaac/l2ss-py/actions/workflows/build-pipeline.yml/badge.svg?branch=main&event=push)](https://github.com/podaac/l2ss-py/actions/workflows/build-pipeline.yml)
+
+Harmony service for subsetting L2 data. l2ss-py supports:
+
+- Spatial subsetting
+    - Bounding box
+    - Shapefile subsetting
+    - GeoJSON subsetting
+- Temporal subsetting
+- Variable subsetting
+- Vertical subsetting
+
+If you would like to contribute to l2ss-py, refer to the [contribution document](CONTRIBUTING.md).
+
+## Initial setup, with poetry
+
+1. Follow the instructions for installing `poetry` [here](https://python-poetry.org/docs/).
+2. Install l2ss-py, with its dependencies, by running the following from the repository directory:
+
+```
+poetry install
+```
+
+***Note:*** l2ss-py can be installed as above and run without any dependency on `harmony`. 
+However, to additionally test the harmony adapter layer, 
+extra dependencies can be installed with `poetry install -E harmony`.
+
+## How to test l2ss-py locally
+
+### Unit tests
+
+There are comprehensive unit tests for l2ss-py. The tests can be run as follows:
+
+```
+poetry run pytest -m "not aws and not integration" tests/
+```
+
+You can generate coverage reports as follows:
+
+```
+poetry run pytest --junitxml=build/reports/pytest.xml --cov=podaac/ --cov-report=html -m "not aws and not integration" tests/
+```
+
+***Note:*** The majority of the tests execute core functionality of l2ss-py without ever interacting with the harmony python modules. 
+The `test_subset_harmony` tests, however, are explicitly for testing the harmony adapter layer 
+and do require the harmony optional dependencies be installed, 
+as described above with the `-E harmony` argument.
+
+### l2ss-py script
+
+You can run l2ss-py on a single granule without using Harmony. In order 
+to run this, the l2ss-py package must be installed in your current 
+Python interpreter
+
+```
+$ l2ss-py --help
+usage: l2ss-py [-h] [--bbox BBOX BBOX BBOX BBOX] [--variables VARIABLES [VARIABLES ...]] [--min-time MIN_TIME] [--max-time MAX_TIME] [--cut] [--shapefile SHAPEFILE] [--pixel_subset] [--vertical-var VERTICAL_VAR] [--vertical-min VERTICAL_MIN] [--vertical-max VERTICAL_MAX]
+               input_file output_file
+
+Run l2ss-py
+
+positional arguments:
+  input_file            File to subset
+  output_file           Output file
+
+options:
+  -h, --help            show this help message and exit
+  --bbox BBOX BBOX BBOX BBOX
+                        Bounding box in the form min_lon min_lat max_lon max_lat
+  --variables VARIABLES [VARIABLES ...]
+                        Variables, only include if variable subset is desired. Should be a space separated list of variable names e.g. sst wind_dir sst_error ...
+  --min-time MIN_TIME   Min time. Should be ISO-8601 format. Only include if temporal subset is desired.
+  --max-time MAX_TIME   Max time. Should be ISO-8601 format. Only include if temporal subset is desired.
+  --cut                 If provided, scanline will be cut
+  --shapefile SHAPEFILE
+                        Path to either shapefile or geojson file used to subset the provided input granule
+  --pixel_subset        To pixel cut based the lon lat on the bounding box
+  --vertical-var VERTICAL_VAR
+                        Name of the vertical variable to subset by (e.g., depth, altitude)
+  --vertical-min VERTICAL_MIN
+                        Minimum value for vertical subsetting (inclusive)
+  --vertical-max VERTICAL_MAX
+                        Maximum value for vertical subsetting (inclusive)
+```
+
+#### Additional subsetting options
+
+The following options are also recorded in the output file's metadata history for provenance and reproducibility:
+- `--min-time` and `--max-time` (temporal subsetting)
+- `--variables` (variable subsetting)
+- `--vertical-var`, `--vertical-min`, `--vertical-max` (vertical subsetting)
+- `--cut`, `--pixel_subset`, `--shapefile`, and `--bbox` (spatial subsetting)
+
+All subsetting parameters used in a run are included in the output file's `history` and `history_json` attributes.
+
+For example:
+
+```
+l2ss-py /path/to/input.nc /path/to/output.nc --bbox -50 -10 50 10 --variables wind_speed wind_dir ice_age time --min-time '2015-07-02T09:00:00' --max-time '2015-07-02T10:00:00' --cut --vertical-var depth --vertical-min 0 --vertical-max 100
+```
+
+An addition to providing a bounding box, spatial subsetting can be achieved by passing in a shapefile or a geojson file. 
+
+```shell script
+poetry run l2ss-py /path/to/input.nc /path/to/output.nc --shapefile /path/to/test.shp
+```
+
+or 
+
+```shell script
+poetry run l2ss-py /path/to/input.nc /path/to/output.nc --shapefile /path/to/test.geojson
+```
+
+### Running Harmony locally
+
+In order to fully test l2ss-py with Harmony, you can run Harmony locally. This requires the data exists in UAT Earthdata Cloud.
+
+1. Set up local Harmony instance. Instructions [here](https://github.com/nasa/harmony#Quick-Start)
+2. Add concept ID for your data to [services.yml](https://github.com/nasa/harmony/blob/main/config/services.yml)
+3. Execute a local Harmony l2ss-py request. For example:
+    ```
+   localhost:3000/YOUR_COLLECTION_ID/ogc-api-coverages/1.0.0/collections/all/coverage/rangeset?format=application%2Fx-netcdf4&subset=lat(-10%3A10)&subset=lon(-10%3A10)&maxResults=2
+   ```
+
+## NASA EOSDIS Integration
+
+Detailed instructions for integrating with EOSDIS can be found [here](EOSDISIntegrations.md).

podaac_l2ss_py-3.3.3/podaac/subsetter/__init__.py

@@ -0,0 +1,11 @@
+# Copyright 2019, by the California Institute of Technology.
+# ALL RIGHTS RESERVED. United States Government Sponsorship acknowledged.
+# Any commercial use must be negotiated with the Office of Technology
+# Transfer at the California Institute of Technology.
+#
+# This software may be subject to U.S. export control laws. By accepting
+# this software, the user agrees to comply with all applicable U.S. export
+# laws and regulations. User has the responsibility to obtain export
+# licenses, or other export authority as may be required before exporting
+# such information to foreign countries or providing access to foreign
+# persons.