switch to a src layout

ASFHyP3 · Oct 20, 2023 · 0acd6ba · 0acd6ba
1 parent 2391757
commit 0acd6ba
Show file tree

Hide file tree

Showing 42 changed files with 20 additions and 17 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,26 +14,26 @@ and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 * `hyp3-autorift` now only uses `pyproject.toml` for package creation now that `setuptools` recommends [not using setup.py](https://setuptools.pypa.io/en/latest/userguide/quickstart.html#setuppy-discouraged).
 
 ### Fixed
-* Patch [235](hyp3_autorift/vend/CHANGES-227.diff) was applied  to make it easier for users to correct for ionosphere
+* Patch [235](src/hyp3_autorift/vend/CHANGES-227.diff) was applied  to make it easier for users to correct for ionosphere
   streaks without needing to know the scale factor.
 
 ## [0.12.0]
 
 ### Added
-* [`hyp3_autorift.crop`](hyp3_autorift/crop.py) provides a `crop_netcdf_product` function to crop HyP3 AutoRIFT products
+* [`hyp3_autorift.crop`](src/hyp3_autorift/crop.py) provides a `crop_netcdf_product` function to crop HyP3 AutoRIFT products
   to the extent of valid `v` data
 
 ### Changed
 * HyP3 AutoRIFT products generated with the main workflow will be cropped to the extent of the valid `v` data
 
 ### Fixed
-* Patch [227](hyp3_autorift/vend/CHANGES-227.diff) was applied to align the S1 granules velocity description with the
+* Patch [227](src/hyp3_autorift/vend/CHANGES-227.diff) was applied to align the S1 granules velocity description with the
   optical products
 
 ## [0.11.1]
 
 ### Fixed
-* Patch [223](hyp3_autorift/vend/CHANGES-223.diff) was applied so that the polarization is correctly selected in the
+* Patch [223](src/hyp3_autorift/vend/CHANGES-223.diff) was applied so that the polarization is correctly selected in the
   sentinel-1 workflow
 
 ## [0.11.0]
@@ -46,7 +46,7 @@ and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
     autoRIFT versions < 0.9.0, which was released November 2, 2022
 
 ### Changed
-* Patch [nasa-jpl/autorift#78](hyp3_autorift/vend/CHANGES-UPSTREAM-78.diff) was applied from upstream to support the
+* Patch [nasa-jpl/autorift#78](src/hyp3_autorift/vend/CHANGES-UPSTREAM-78.diff) was applied from upstream to support the
   Sentinel-1 correction workflow
 
 ### Removed
@@ -76,14 +76,14 @@ and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ### Changed
 
-* Patch [196](hyp3_autorift/vend/CHANGES-189.diff) was applied to update the `flag_meanings` netCDF attribute to be
-  inline with CF-Convention 1.8, as described in the [vendored software README.md](hyp3_autorift/vend/README.md)
+* Patch [196](src/hyp3_autorift/vend/CHANGES-189.diff) was applied to update the `flag_meanings` netCDF attribute to be
+  inline with CF-Convention 1.8, as described in the [vendored software README.md](src/hyp3_autorift/vend/README.md)
 
 ## [0.10.1]
 
 ### Changed
-* Patches [189](hyp3_autorift/vend/CHANGES-189.diff),  [191](hyp3_autorift/vend/CHANGES-191.diff), and [194](hyp3_autorift/vend/CHANGES-194.diff) 
-  were applied to update some netCDF variable attributes, as described in the [vendored software README.md](hyp3_autorift/vend/README.md)
+* Patches [189](src/hyp3_autorift/vend/CHANGES-189.diff),  [191](src/hyp3_autorift/vend/CHANGES-191.diff), and [194](src/hyp3_autorift/vend/CHANGES-194.diff) 
+  were applied to update some netCDF variable attributes, as described in the [vendored software README.md](src/hyp3_autorift/vend/README.md)
 
 ## [0.10.0]
 
@@ -98,8 +98,8 @@ and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 ## [0.9.1]
 
 ### Changed
-* [A patch](hyp3_autorift/vend/CHANGES-176.diff) was applied to update some netCDF variable attributes, as described
-  in the [vendored software README.md](hyp3_autorift/vend/README.md)
+* [A patch](src/hyp3_autorift/vend/CHANGES-176.diff) was applied to update some netCDF variable attributes, as described
+  in the [vendored software README.md](src/hyp3_autorift/vend/README.md)
 
 ## [0.9.0]
 
@@ -173,7 +173,7 @@ and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ### Changed
 * Patches were applied to clean up some netCDF variable attributes, as described
-  in the [vendored software README.md](hyp3_autorift/vend/README.md)
+  in the [vendored software README.md](src/hyp3_autorift/vend/README.md)
 
 ## [0.7.3](https://github.com/ASFHyP3/hyp3-autorift/compare/v0.7.2...v0.7.3)
 
@@ -183,14 +183,14 @@ and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 * In the netCDF product, the default autoRIFT parameter file URL will always be reported
   instead of reporting copies used to support custom HyP3 deployments
 * A patch was applied to fix some Sentinel-1 and Sentinel-2 product metadata, as described
-  in the [vendored software README.md](hyp3_autorift/vend/README.md)
+  in the [vendored software README.md](src/hyp3_autorift/vend/README.md)
 
 ### Fixed
 * Updated the upgrade to autoRIFT `v1.4.0` to account for the autoRIFT source repo
   having moved the `v1.4.0` tag  (between commits [`67e4996..b6700f9`](https://github.com/nasa-jpl/autoRIFT/compare/67e4996..b6700f9))
   and changed the conda-forge package accordingly (new sha256 and bumped the build number).
   * The autoRIFT workflow scripts are now based on the moved tag and any still
-    necessary fixes were applied as described in the [vendored software README.md](hyp3_autorift/vend/README.md)
+    necessary fixes were applied as described in the [vendored software README.md](src/hyp3_autorift/vend/README.md)
 * For Sentinel-2 products, file names now include the full COG Id to ensure unique
   file names are produced and to be consistent with other products.
 
@@ -203,15 +203,15 @@ and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ### Changed
 * Applied a fix to the autoRIFT packaging script that updates the reference velocity
-  fields for projected velocity, as described in the [vendored software README.md](hyp3_autorift/vend/README.md)
+  fields for projected velocity, as described in the [vendored software README.md](src/hyp3_autorift/vend/README.md)
 
 ## [0.7.0](https://github.com/ASFHyP3/hyp3-autorift/compare/v0.6.3...v0.7.0)
 
 ### Changed
 * Upgraded autoRIFT to [v1.4.0](https://github.com/leiyangleon/autoRIFT/releases/tag/v1.4.0)
   and [ISCE2 v2.5.3 built with autoRIFT v1.4.0](https://anaconda.org/hyp3/isce2)
 * Applied some fixes to the autoRIFT workflow scripts as described in the
-  [vendored software README.md](hyp3_autorift/vend/README.md)
+  [vendored software README.md](src/hyp3_autorift/vend/README.md)
 * `hyp3_autorift.io.save_topsinsar_mat` has been renamed to `hyp3_autorift.io.get_topsinsar_config`
   * It no longer writes a config `.mat` file and instead returns the config dictionary
 
@@ -225,7 +225,7 @@ and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ### Changed
 * Applied some minor error estimate fixes and netCDF metadata attribute updates as
-  described in the [vendored software README.md](hyp3_autorift/vend/README.md)
+  described in the [vendored software README.md](src/hyp3_autorift/vend/README.md)
 * `process.get_lc2_metadata()` now attempts to fetch STAC metadata from the
   https://landsatlook.usgs.gov/ API and falls back the STAC json in the S3 bucket
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -63,4 +63,7 @@ Documentation = "https://hyp3-docs.asf.alaska.edu"
 include-package-data = true
 zip-safe = false
 
+[tool.setuptools.packages.find]
+where = ["src"]
+
 [tool.setuptools_scm]
diff --git a/hyp3_autorift/__init__.py → src/hyp3_autorift/__init__.py b/hyp3_autorift/__init__.py → src/hyp3_autorift/__init__.py
diff --git a/hyp3_autorift/__main__.py → src/hyp3_autorift/__main__.py b/hyp3_autorift/__main__.py → src/hyp3_autorift/__main__.py
diff --git a/hyp3_autorift/crop.py → src/hyp3_autorift/crop.py b/hyp3_autorift/crop.py → src/hyp3_autorift/crop.py
diff --git a/hyp3_autorift/etc/entrypoint.sh → src/hyp3_autorift/etc/entrypoint.sh b/hyp3_autorift/etc/entrypoint.sh → src/hyp3_autorift/etc/entrypoint.sh
diff --git a/hyp3_autorift/geometry.py → src/hyp3_autorift/geometry.py b/hyp3_autorift/geometry.py → src/hyp3_autorift/geometry.py
diff --git a/hyp3_autorift/image.py → src/hyp3_autorift/image.py b/hyp3_autorift/image.py → src/hyp3_autorift/image.py
diff --git a/hyp3_autorift/io.py → src/hyp3_autorift/io.py b/hyp3_autorift/io.py → src/hyp3_autorift/io.py
diff --git a/hyp3_autorift/process.py → src/hyp3_autorift/process.py b/hyp3_autorift/process.py → src/hyp3_autorift/process.py
diff --git a/hyp3_autorift/s1_correction.py → src/hyp3_autorift/s1_correction.py b/hyp3_autorift/s1_correction.py → src/hyp3_autorift/s1_correction.py
diff --git a/hyp3_autorift/vend/CHANGES-173.diff → src/hyp3_autorift/vend/CHANGES-173.diff b/hyp3_autorift/vend/CHANGES-173.diff → src/hyp3_autorift/vend/CHANGES-173.diff
diff --git a/hyp3_autorift/vend/CHANGES-176.diff → src/hyp3_autorift/vend/CHANGES-176.diff b/hyp3_autorift/vend/CHANGES-176.diff → src/hyp3_autorift/vend/CHANGES-176.diff
diff --git a/hyp3_autorift/vend/CHANGES-183.diff → src/hyp3_autorift/vend/CHANGES-183.diff b/hyp3_autorift/vend/CHANGES-183.diff → src/hyp3_autorift/vend/CHANGES-183.diff
diff --git a/hyp3_autorift/vend/CHANGES-189.diff → src/hyp3_autorift/vend/CHANGES-189.diff b/hyp3_autorift/vend/CHANGES-189.diff → src/hyp3_autorift/vend/CHANGES-189.diff
diff --git a/hyp3_autorift/vend/CHANGES-191.diff → src/hyp3_autorift/vend/CHANGES-191.diff b/hyp3_autorift/vend/CHANGES-191.diff → src/hyp3_autorift/vend/CHANGES-191.diff
diff --git a/hyp3_autorift/vend/CHANGES-194.diff → src/hyp3_autorift/vend/CHANGES-194.diff b/hyp3_autorift/vend/CHANGES-194.diff → src/hyp3_autorift/vend/CHANGES-194.diff
diff --git a/hyp3_autorift/vend/CHANGES-196.diff → src/hyp3_autorift/vend/CHANGES-196.diff b/hyp3_autorift/vend/CHANGES-196.diff → src/hyp3_autorift/vend/CHANGES-196.diff
diff --git a/hyp3_autorift/vend/CHANGES-211.diff → src/hyp3_autorift/vend/CHANGES-211.diff b/hyp3_autorift/vend/CHANGES-211.diff → src/hyp3_autorift/vend/CHANGES-211.diff
diff --git a/hyp3_autorift/vend/CHANGES-213.diff → src/hyp3_autorift/vend/CHANGES-213.diff b/hyp3_autorift/vend/CHANGES-213.diff → src/hyp3_autorift/vend/CHANGES-213.diff
diff --git a/hyp3_autorift/vend/CHANGES-214.diff → src/hyp3_autorift/vend/CHANGES-214.diff b/hyp3_autorift/vend/CHANGES-214.diff → src/hyp3_autorift/vend/CHANGES-214.diff
diff --git a/hyp3_autorift/vend/CHANGES-223.diff → src/hyp3_autorift/vend/CHANGES-223.diff b/hyp3_autorift/vend/CHANGES-223.diff → src/hyp3_autorift/vend/CHANGES-223.diff
diff --git a/hyp3_autorift/vend/CHANGES-227.diff → src/hyp3_autorift/vend/CHANGES-227.diff b/hyp3_autorift/vend/CHANGES-227.diff → src/hyp3_autorift/vend/CHANGES-227.diff
diff --git a/hyp3_autorift/vend/CHANGES-235.diff → src/hyp3_autorift/vend/CHANGES-235.diff b/hyp3_autorift/vend/CHANGES-235.diff → src/hyp3_autorift/vend/CHANGES-235.diff
diff --git a/hyp3_autorift/vend/CHANGES-UPSTREAM-78.diff → ...p3_autorift/vend/CHANGES-UPSTREAM-78.diff b/hyp3_autorift/vend/CHANGES-UPSTREAM-78.diff → ...p3_autorift/vend/CHANGES-UPSTREAM-78.diff
diff --git a/hyp3_autorift/vend/CHANGES.diff → src/hyp3_autorift/vend/CHANGES.diff b/hyp3_autorift/vend/CHANGES.diff → src/hyp3_autorift/vend/CHANGES.diff
diff --git a/hyp3_autorift/vend/LICENSE → src/hyp3_autorift/vend/LICENSE b/hyp3_autorift/vend/LICENSE → src/hyp3_autorift/vend/LICENSE
diff --git a/hyp3_autorift/vend/README.md → src/hyp3_autorift/vend/README.md b/hyp3_autorift/vend/README.md → src/hyp3_autorift/vend/README.md
diff --git a/hyp3_autorift/vend/__init__.py → src/hyp3_autorift/vend/__init__.py b/hyp3_autorift/vend/__init__.py → src/hyp3_autorift/vend/__init__.py
diff --git a/hyp3_autorift/vend/netcdf_output.py → src/hyp3_autorift/vend/netcdf_output.py b/hyp3_autorift/vend/netcdf_output.py → src/hyp3_autorift/vend/netcdf_output.py
diff --git a/hyp3_autorift/vend/testGeogridOptical.py → src/hyp3_autorift/vend/testGeogridOptical.py b/hyp3_autorift/vend/testGeogridOptical.py → src/hyp3_autorift/vend/testGeogridOptical.py
diff --git a/hyp3_autorift/vend/testGeogrid_ISCE.py → src/hyp3_autorift/vend/testGeogrid_ISCE.py b/hyp3_autorift/vend/testGeogrid_ISCE.py → src/hyp3_autorift/vend/testGeogrid_ISCE.py
diff --git a/hyp3_autorift/vend/testautoRIFT.py → src/hyp3_autorift/vend/testautoRIFT.py b/hyp3_autorift/vend/testautoRIFT.py → src/hyp3_autorift/vend/testautoRIFT.py
diff --git a/hyp3_autorift/vend/testautoRIFT_ISCE.py → src/hyp3_autorift/vend/testautoRIFT_ISCE.py b/hyp3_autorift/vend/testautoRIFT_ISCE.py → src/hyp3_autorift/vend/testautoRIFT_ISCE.py
diff --git a/hyp3_autorift/vend/topsinsar_filename.py → src/hyp3_autorift/vend/topsinsar_filename.py b/hyp3_autorift/vend/topsinsar_filename.py → src/hyp3_autorift/vend/topsinsar_filename.py
diff --git a/hyp3_autorift/vend/workflow/README.md → src/hyp3_autorift/vend/workflow/README.md b/hyp3_autorift/vend/workflow/README.md → src/hyp3_autorift/vend/workflow/README.md
diff --git a/..._autorift/vend/workflow/bbox_dem_trunc.py → ..._autorift/vend/workflow/bbox_dem_trunc.py b/..._autorift/vend/workflow/bbox_dem_trunc.py → ..._autorift/vend/workflow/bbox_dem_trunc.py
diff --git a/hyp3_autorift/vend/workflow/dloadOrbits.py → ...yp3_autorift/vend/workflow/dloadOrbits.py b/hyp3_autorift/vend/workflow/dloadOrbits.py → ...yp3_autorift/vend/workflow/dloadOrbits.py
diff --git a/...autorift/vend/workflow/format_tops_xml.py → ...autorift/vend/workflow/format_tops_xml.py b/...autorift/vend/workflow/format_tops_xml.py → ...autorift/vend/workflow/format_tops_xml.py
diff --git a/hyp3_autorift/vend/workflow/prepDEM.py → src/hyp3_autorift/vend/workflow/prepDEM.py b/hyp3_autorift/vend/workflow/prepDEM.py → src/hyp3_autorift/vend/workflow/prepDEM.py
diff --git a/...ow/single_scene_proc_S1A_fetchDEM_full.py → ...ow/single_scene_proc_S1A_fetchDEM_full.py b/...ow/single_scene_proc_S1A_fetchDEM_full.py → ...ow/single_scene_proc_S1A_fetchDEM_full.py
diff --git a/...ingle_scene_proc_optical_fetchDEM_full.py → ...ingle_scene_proc_optical_fetchDEM_full.py b/...ingle_scene_proc_optical_fetchDEM_full.py → ...ingle_scene_proc_optical_fetchDEM_full.py