Merge branch 'main' into feature/dockerized-environment

Clay-foundation · Jun 7, 2024 · 30f01c3 · 30f01c3
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diff --git a/docs/_toc.yml b/docs/_toc.yml
@@ -6,12 +6,12 @@ root: index
 parts:
 - caption: Release notes
   chapters:
-    - title: Software release notes
-      file: release-notes/changelog
     - title: Model release notes
       file: release-notes/specification
     - title: Data sampling strategy
       file: release-notes/data_sampling
+    - title: Software release notes v1.0
+      file: release-notes/changelog-v1.0
 - caption: Getting Started
   chapters:
     - title: Installation
@@ -53,3 +53,5 @@ parts:
       - title: Benchmark dataset labels
         file: clay-v0/data_labels
       - file: clay-v0-interpolation
+      - title: Software release notes v0.1
+        file: clay-v0/changelog-v1.0
diff --git a/docs/release-notes/changelog.md → docs/clay-v0/changelog-v0.1.md b/docs/release-notes/changelog.md → docs/clay-v0/changelog-v0.1.md
@@ -1,4 +1,4 @@
-(software_release)=
+(software_release_v0)=
 # Code Model release v0.0.1
 
 This changelog is a summary of the changes to the source code of the Clay model.

diff --git a/docs/clay-v0/specification-v0.md b/docs/clay-v0/specification-v0.md
@@ -5,7 +5,7 @@ This changelog is a summary of the changes to the pretrained model weights for t
 
 Model weights released on 2024/01/12.
 
-> For release notes for the source code, see [](software_release)
+> For release notes for the source code, see [](software_release_v0)
 
 ### Summary
 

diff --git a/docs/release-notes/changelog-v1.0.md b/docs/release-notes/changelog-v1.0.md
@@ -0,0 +1,76 @@
+(software_release_v1)=
+# Release v1.0 (2024/06/06)
+
+## 💫 Highlights
+
+* 🎉 **Release of Clay Foundation Model v1.0** 🎉
+
+## 🚀 Model
+
+* Datamodule & Model for Clay v1 by @srmsoumya in https://github.com/Clay-foundation/model/pull/253
+
+## 🗃️ Data Pipeline
+
+* Moved data pipeline code into [stacchip](https://github.com/Clay-foundation/stacchip) a dedicated library for the data wrangling
+
+## 📖 Documentation
+
+* Clay over aoi by @yellowcap in https://github.com/Clay-foundation/model/pull/116
+* Convert run-over-aoi ipynb to md by @yellowcap in https://github.com/Clay-foundation/model/pull/122
+* Static Documentation for v0.1 by @brunosan in https://github.com/Clay-foundation/model/pull/118
+* Document data sampling strategy by @yellowcap in https://github.com/Clay-foundation/model/pull/124
+* Updating location to download imagery script in docs by @MaxLenormand in https://github.com/Clay-foundation/model/pull/198
+* Change "Radiant Earth Foundation" to "Radiant Earth" in docs by @kbgg in https://github.com/Clay-foundation/model/pull/214
+* Update instructions to re-lock conda-lock.yml file by @weiji14 in https://github.com/Clay-foundation/model/pull/225
+* chore(docs): correct typos and improve stylistic consistency by @kelseyjosund in https://github.com/Clay-foundation/model/pull/232
+* Partial inputs - Pakistan flood tutorial by @lillythomas in https://github.com/Clay-foundation/model/pull/154
+* Obtain patch level metadata (e.g. geospatial bounds and cloud cover), save and demo DEP use case (sim search) by @lillythomas in https://github.com/Clay-foundation/model/pull/172
+* Obtain patch level cloud coverage percentages by @lillythomas in https://github.com/Clay-foundation/model/pull/184
+* Tutorial on burn scar analysis using embeddings from partial inputs by @yellowcap in https://github.com/Clay-foundation/model/pull/149
+* Doc updates by @brunosan in https://github.com/Clay-foundation/model/pull/230
+* Update specification.md by @brunosan in https://github.com/Clay-foundation/model/pull/250
+* Add notebook showing how to run v1 by @yellowcap in https://github.com/Clay-foundation/model/pull/254
+* Documented v1 sampling strategy by @yellowcap in https://github.com/Clay-foundation/model/pull/249
+* Updates the mamba install instructions link. by @dbonomo in https://github.com/Clay-foundation/model/pull/252
+* Remove clay-v0-tutorials & add visualize embeddings for v1 by @srmsoumya in https://github.com/Clay-foundation/model/pull/256
+* Minor spelling fix by @tylere in https://github.com/Clay-foundation/model/pull/260
+* Shorten comment line length by @yellowcap in https://github.com/Clay-foundation/model/pull/261
+* Refactor docs by moving v0 docs into separate section by @yellowcap in https://github.com/Clay-foundation/model/pull/262
+* Docs v1 continued by @yellowcap in https://github.com/Clay-foundation/model/pull/263
+* Documented metadata file for normalization and wavelenghts by @yellowcap in https://github.com/Clay-foundation/model/pull/266
+* [small change] add source.coop link by @brunosan in https://github.com/Clay-foundation/model/pull/137
+* Segmentation on Clay by @srmsoumya in https://github.com/Clay-foundation/model/pull/257
+
+## 🧰 Maintenance
+
+* [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/Clay-foundation/model/pull/206
+* Bump conda-lock from 2.5.1 to 2.5.6 by @weiji14 in https://github.com/Clay-foundation/model/pull/183
+* Remove scripts folder by @yellowcap in https://github.com/Clay-foundation/model/pull/265
+* Unified v1 and v0 environments by @yellowcap in https://github.com/Clay-foundation/model/pull/264
+* Add osx-arm64 platform to conda-lock.yml file and GitHub Actions CI by @weiji14 in https://github.com/Clay-foundation/model/pull/164
+* Move pipeline scripts into dedicated folder by @yellowcap in https://github.com/Clay-foundation/model/pull/163
+* Memory buildup clean by @brunosan in https://github.com/Clay-foundation/model/pull/158
+* Add osx platform to conda lock file and CI by @chuckwondo in https://github.com/Clay-foundation/model/pull/162
+* Add scikit-learn by @weiji14 in https://github.com/Clay-foundation/model/pull/159
+* Remove float16 dype in favor of float32 by @yellowcap in https://github.com/Clay-foundation/model/pull/143
+* Remove stale bands argument from clay model classes by @yellowcap in https://github.com/Clay-foundation/model/pull/144
+
+## :hammer_and_wrench: v0.2 updates
+
+* Add normalization parameters to documentation by @yellowcap in https://github.com/Clay-foundation/model/pull/152
+* Worldcover embeddings conus by @yellowcap in https://github.com/Clay-foundation/model/pull/153
+* Create data/minicubes directory if it doesn't already exist by @weiji14 in https://github.com/Clay-foundation/model/pull/160
+* Clay pipeline v04 by @yellowcap in https://github.com/Clay-foundation/model/pull/173
+* Shuffle patches only during training by @yellowcap in https://github.com/Clay-foundation/model/pull/135
+* Add option to output raw patch embeddings by @yellowcap in https://github.com/Clay-foundation/model/pull/133
+
+## 🧑‍🤝‍🧑 New Contributors
+
+* @chuckwondo made their first contribution in https://github.com/Clay-foundation/model/pull/162
+* @MaxLenormand made their first contribution in https://github.com/Clay-foundation/model/pull/198
+* @kbgg made their first contribution in https://github.com/Clay-foundation/model/pull/214
+* @kelseyjosund made their first contribution in https://github.com/Clay-foundation/model/pull/232
+* @dbonomo made their first contribution in https://github.com/Clay-foundation/model/pull/252
+* @tylere made their first contribution in https://github.com/Clay-foundation/model/pull/260
+
+**Full Changelog**: https://github.com/Clay-foundation/model/compare/v0.0.1...v1.0
diff --git a/docs/release-notes/specification.md b/docs/release-notes/specification.md
@@ -4,7 +4,7 @@ This changelog is a summary of the changes to the pretrained model weights for t
 
 Model weights released on 2024/05/12.
 
-> For release notes for the source code, see [](software_release)
+> For release notes for the source code, see [](software_release_v1)
 
 ## Summary
 

diff --git a/finetune/segment/chesapeake_datamodule.py b/finetune/segment/chesapeake_datamodule.py
@@ -89,10 +89,6 @@ def __getitem__(self, idx):
         label_mapping = {1: 0, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 15: 6}
         remapped_label = np.vectorize(label_mapping.get)(label)
 
-        # Apply transformations
-        if self.transform:
-            chip = self.transform(torch.from_numpy(chip))
-
         sample = {
             "pixels": self.transform(torch.from_numpy(chip)),
             "label": torch.from_numpy(remapped_label[0]),